1 Introduction
Though there is no fundamental reason to separate the likelihood ratio testing and GSVA from the differential expression analyses, they are both tasks which reach back to the primary expression data, unlike GSEA. Therefore I chose to separate these two tasks into a their own document.
2 LRT
The likelihood ratio testing performed on the TMRC3 data is intended to look for shared patterns of expression across some known, constant factor. This may be time (are there patterns across the visits of each person), or cell type (do some genes act consistently across type). We could also ask this question of our two clinics, or indeed across the cure/fail samples.
2.1 Patterns across clinic
tc_clinical_filt <- normalize_expt(tc_clinical, filter = TRUE)## Removing 5633 low-count genes (14290 remaining).tc_lrt_clinic <- deseq_lrt(tc_clinical_filt, transform = "vst", interaction = FALSE,
interactor_column = "visitnumber",
interest_column = "clinic")## Warning in deseq_lrt(tc_clinical_filt, transform = "vst", interaction = FALSE, :
## The clinic should probably be a factor, set it with the 'factors' arg.## converting counts to integer mode## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factors## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 169 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing## A large number of genes was given-- please, make sure this is not an error. Normally, only DE genes will be useful for this function.## Working with 6272 genes.## Working with 6269 genes after filtering: minc > 3## Joining, by = "merge"
## Joining, by = "merge"
summary(lrt_visit[["favorite_genes"]])## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'summary': object 'lrt_visit' not foundt_clinical_filt <- normalize_expt(t_clinical, filter=TRUE)## Removing 5774 low-count genes (14149 remaining).lrt_visit <- deseq_lrt(t_clinical_filt, transform = "vst", interaction = FALSE,
interactor_column = "visitnumber",
interest_column = "finaloutcome")## converting counts to integer mode## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 120 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing## A large number of genes was given-- please, make sure this is not an error. Normally, only DE genes will be useful for this function.## Working with 5439 genes.## Working with 5435 genes after filtering: minc > 3## Joining, by = "merge"
## Joining, by = "merge"
summary(lrt_visit[["favorite_genes"]])## genes cluster
## Length:5435 Min. : 1.00
## Class :character 1st Qu.: 2.00
## Mode :character Median : 3.00
## Mean : 3.46
## 3rd Qu.: 3.00
## Max. :11.00written <- write_xlsx(data = as.data.frame(lrt_visit[["deseq_table"]]),
excel = glue::glue("excel/lrt_clinical_visit-v{ver}.xlsx"))
lrt_monocyte_visit <- deseq_lrt(t_visitcf_monocyte, transform = "vst",
interaction = FALSE,
interactor_column = "visitnumber",
interest_column = "finaloutcome")## converting counts to integer mode
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 68 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
## Working with 12 genes.
## Working with 12 genes after filtering: minc > 3
## Joining, by = "merge"Joining, by = "merge"
lrt_monocyte_visit$cluster_data$plot
lrt_monocyte_visit_v2 <- deseq_lrt(t_visitcf_monocyte, transform = "vst",
interaction = FALSE, minc = 1,
interactor_column = "visitnumber",
interest_column = "finaloutcome")## converting counts to integer mode
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 68 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
## Working with 12 genes.
## Working with 12 genes after filtering: minc > 1
## Joining, by = "merge"Joining, by = "merge"
2.2 Shared patterns across cell types
lrt_celltype_clinical_test <- deseq_lrt(tc_clinical, transform = "vst",
interactor_column = "typeofcells",
interest_column = "finaloutcome")## converting counts to integer mode## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 15 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing## Working with 552 genes.## Working with 551 genes after filtering: minc > 3## Joining, by = "merge"
## Joining, by = "merge"
hs_annot <- fData(hs_expt)
deseq_lrt_df <- merge(hs_annot, as.data.frame(lrt_celltype_clinical_test[["deseq_table"]]), all.y=TRUE,
by="row.names")
rownames(deseq_lrt_df) <- deseq_lrt_df[["Row.names"]]
deseq_lrt_df[["Row.names"]] <- NULL
written <- write_xlsx(data=deseq_lrt_df,
excel=glue::glue("excel/lrt_clinical_celltype-v{ver}.xlsx"))3 GSVA
3.1 Load some signatures
If one chooses, simple_gsva() can either load signatures from the GSVAdata package, which is a little old, or load an arbitrary set. load_gmt_signatures() provides a quick way to extract them from a gmt file.
broad_c7 <- load_gmt_signatures(signatures="reference/msigdb/c7.all.v7.5.1.entrez.gmt",
signature_category="c7")
broad_c2 <- load_gmt_signatures(signatures="reference/msigdb/c2.all.v7.5.1.entrez.gmt",
signature_category="c2")
broad_h <- load_gmt_signatures(signatures="reference/msigdb/h.all.v7.5.1.entrez.gmt",
signature_category="h")3.1.1 Clinical samples
3.1.1.1 Clinical C2
tc_celltype_gsva_c2 <- simple_gsva(
tc_valid, signatures=broad_c2,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 6353 rownames shared with the gsva result out of 6353.tc_celltype_gsva_c2_sig <- get_sig_gsva_categories(
tc_celltype_gsva_c2,
excel="analyses/3_cali_and_tumaco/GSVA/tc_valid_gsva_c2.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: failure_vs_cure. Adjust = BH## Limma step 6/6: 1/2: Creating table: cure. Adjust = BH## Limma step 6/6: 2/2: Creating table: failure. Adjust = BH## The factor cure has 122 rows.## The factor failure has 62 rows.## plot labels was not set and there are more than 100 samples, disabling it.## Testing each factor against the others.## Scoring cure against everything else.## Scoring failure against everything else.## Deleting the file analyses/3_cali_and_tumaco/GSVA/tc_valid_gsva_c2.xlsx before writing the tables.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 203395_s_at,HES1 ... 4_s_at,CTBS,1486 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : NUP42,11097|1654 ... 4_at,UBE2D3,7323 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2|39449_at,,|355 ... 14_at,UBA2,10054 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : t,NUFIP1,26747|2 ... x_at,EEF1A1,1915 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ENSG00000273641, ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 16224|Arid4b,ARI ... gcs1,HMGCS1,3157 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 643180|218637_at ... 0_s_at,NREP,9315 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |219698_s_at,MET ... _at,TMEM97,27346 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 343|ENSG00000182 ... 499,FAM20C,56975 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ,51283|1442393_a ... 11_s_at,DBP,1628 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 7|ENSG0000019736 ... 000288631,162699 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2804,KRTAP10-7,3 ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 701_s_at,CHCHD7, ... 0_at,SH2B3,10019 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 101927051|204365 ... _at,EPS8L2,64787 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |rc_AA957218_at, ... 8|rc_H33093_at,, is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 824,HDGFL1,15415 ... 7495,TMED3,23423 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : L2,27039|8108287 ... 7,CCDC187,399693 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2|39449_at,,|355 ... 14_at,UBA2,10054 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ENSG00000273641, ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : NUP42,11097|1654 ... 4_at,UBE2D3,7323 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : t,NUFIP1,26747|2 ... x_at,EEF1A1,1915 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 16224|Arid4b,ARI ... gcs1,HMGCS1,3157 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 203395_s_at,HES1 ... 4_s_at,CTBS,1486 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 343|ENSG00000182 ... 499,FAM20C,56975 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ,51283|1442393_a ... 11_s_at,DBP,1628 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 643180|218637_at ... 0_s_at,NREP,9315 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |219698_s_at,MET ... _at,TMEM97,27346 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 7|ENSG0000019736 ... 000288631,162699 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 701_s_at,CHCHD7, ... 0_at,SH2B3,10019 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2804,KRTAP10-7,3 ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 101927051|204365 ... _at,EPS8L2,64787 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |rc_AA957218_at, ... 8|rc_H33093_at,, is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 824,HDGFL1,15415 ... 7495,TMED3,23423 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : L2,27039|8108287 ... 7,CCDC187,399693 is truncated.
## Number of characters exeed the limit of 32767.tc_celltype_gsva_c2_sig$subset_plottc_celltype_gsva_c2_sig$score_plot3.1.1.2 Valid C7
tc_celltype_gsva_c7 <- simple_gsva(
tc_valid, signatures=broad_c7,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
signature_category="c7")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 5209 rownames shared with the gsva result out of 5209.tc_celltype_gsva_c7_sig <- get_sig_gsva_categories(
tc_celltype_gsva_c7,
excel="analyses/3_cali_and_tumaco/GSVA/tc_valid_gsva_c7.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: failure_vs_cure. Adjust = BH## Limma step 6/6: 1/2: Creating table: cure. Adjust = BH## Limma step 6/6: 2/2: Creating table: failure. Adjust = BH## The factor cure has 122 rows.## The factor failure has 62 rows.## plot labels was not set and there are more than 100 samples, disabling it.## Testing each factor against the others.## Scoring cure against everything else.## Scoring failure against everything else.## Deleting the file analyses/3_cali_and_tumaco/GSVA/tc_valid_gsva_c7.xlsx before writing the tables.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 0750246|PRDM5,PR ... 9|OAS1,OAS1,4938 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 84296|PLEKHA1,PL ... 20H1,KMT5B,51111 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 0750246|PRDM5,PR ... 9|OAS1,OAS1,4938 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 84296|PLEKHA1,PL ... 20H1,KMT5B,51111 is truncated.
## Number of characters exeed the limit of 32767.3.1.1.3 Valid H
tc_celltype_gsva_h <- simple_gsva(
tc_valid,
signatures=broad_h,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
signature_category="h")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 50 rownames shared with the gsva result out of 50.tc_celltype_gsva_h_sig <- get_sig_gsva_categories(
tc_celltype_gsva_h,
excel="analyses/3_cali_and_tumaco/GSVA/tc_valid_gsva_h.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: failure_vs_cure. Adjust = BH## Limma step 6/6: 1/2: Creating table: cure. Adjust = BH## Limma step 6/6: 2/2: Creating table: failure. Adjust = BH## The factor cure has 122 rows.## The factor failure has 62 rows.## plot labels was not set and there are more than 100 samples, disabling it.## Testing each factor against the others.## Scoring cure against everything else.## Scoring failure against everything else.## Deleting the file analyses/3_cali_and_tumaco/GSVA/tc_valid_gsva_h.xlsx before writing the tables.3.1.2 Tumaco samples
3.1.2.1 Clinical C2
t_clinical_gsva_c2 <- simple_gsva(
t_clinical,
signatures=broad_c2,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
signature_category="c2")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 6353 rownames shared with the gsva result out of 6353.t_clinical_gsva_c2_sig <- get_sig_gsva_categories(
t_clinical_gsva_c2,
excel="analyses/4_tumaco/GSVA/t_clinical_gsva_c2.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: failure_vs_cure. Adjust = BH## Limma step 6/6: 1/2: Creating table: cure. Adjust = BH## Limma step 6/6: 2/2: Creating table: failure. Adjust = BH## The factor cure has 67 rows.## The factor failure has 56 rows.## plot labels was not set and there are more than 100 samples, disabling it.## Testing each factor against the others.## Scoring cure against everything else.## Scoring failure against everything else.## Deleting the file analyses/4_tumaco/GSVA/t_clinical_gsva_c2.xlsx before writing the tables.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : t,NUFIP1,26747|2 ... x_at,EEF1A1,1915 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2|39449_at,,|355 ... 14_at,UBA2,10054 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : NUP42,11097|1654 ... 4_at,UBE2D3,7323 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 203395_s_at,HES1 ... 4_s_at,CTBS,1486 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ENSG00000273641, ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 16224|Arid4b,ARI ... gcs1,HMGCS1,3157 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 643180|218637_at ... 0_s_at,NREP,9315 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ,51283|1442393_a ... 11_s_at,DBP,1628 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 343|ENSG00000182 ... 499,FAM20C,56975 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |219698_s_at,MET ... _at,TMEM97,27346 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 7|ENSG0000019736 ... 000288631,162699 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2804,KRTAP10-7,3 ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 701_s_at,CHCHD7, ... 0_at,SH2B3,10019 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 101927051|204365 ... _at,EPS8L2,64787 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |rc_AA957218_at, ... 8|rc_H33093_at,, is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 824,HDGFL1,15415 ... 7495,TMED3,23423 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : L2,27039|8108287 ... 7,CCDC187,399693 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2|39449_at,,|355 ... 14_at,UBA2,10054 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ENSG00000273641, ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : NUP42,11097|1654 ... 4_at,UBE2D3,7323 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : t,NUFIP1,26747|2 ... x_at,EEF1A1,1915 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 16224|Arid4b,ARI ... gcs1,HMGCS1,3157 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 203395_s_at,HES1 ... 4_s_at,CTBS,1486 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 343|ENSG00000182 ... 499,FAM20C,56975 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ,51283|1442393_a ... 11_s_at,DBP,1628 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 643180|218637_at ... 0_s_at,NREP,9315 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |219698_s_at,MET ... _at,TMEM97,27346 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 7|ENSG0000019736 ... 000288631,162699 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 701_s_at,CHCHD7, ... 0_at,SH2B3,10019 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2804,KRTAP10-7,3 ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 101927051|204365 ... _at,EPS8L2,64787 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |rc_AA957218_at, ... 8|rc_H33093_at,, is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 824,HDGFL1,15415 ... 7495,TMED3,23423 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : L2,27039|8108287 ... 7,CCDC187,399693 is truncated.
## Number of characters exeed the limit of 32767.t_clinical_gsva_c2_sig$subset_plot
t_clinical_gsva_c2_sig$score_plot
3.1.2.2 Clinical C7
t_clinical_gsva_c7 <- simple_gsva(
t_clinical,
signatures=broad_c7,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
signature_category="c7")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 5209 rownames shared with the gsva result out of 5209.t_clinical_gsva_c7_sig <- get_sig_gsva_categories(
t_clinical_gsva_c7,
excel="analyses/4_tumaco/GSVA/t_clinical_gsva_c7.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: failure_vs_cure. Adjust = BH## Limma step 6/6: 1/2: Creating table: cure. Adjust = BH## Limma step 6/6: 2/2: Creating table: failure. Adjust = BH## The factor cure has 67 rows.## The factor failure has 56 rows.## plot labels was not set and there are more than 100 samples, disabling it.## Testing each factor against the others.## Scoring cure against everything else.## Scoring failure against everything else.## Deleting the file analyses/4_tumaco/GSVA/t_clinical_gsva_c7.xlsx before writing the tables.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 0750246|PRDM5,PR ... 9|OAS1,OAS1,4938 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 84296|PLEKHA1,PL ... 20H1,KMT5B,51111 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 0750246|PRDM5,PR ... 9|OAS1,OAS1,4938 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 84296|PLEKHA1,PL ... 20H1,KMT5B,51111 is truncated.
## Number of characters exeed the limit of 32767.3.1.2.3 Clinical H
t_clinical_gsva_h <- simple_gsva(
t_clinical,
signatures=broad_h,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
signature_category="h")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 50 rownames shared with the gsva result out of 50.t_clinical_gsva_h_sig <- get_sig_gsva_categories(
t_clinical_gsva_h,
excel="analyses/4_tumaco/GSVA/t_clinical_gsva_h.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: failure_vs_cure. Adjust = BH## Limma step 6/6: 1/2: Creating table: cure. Adjust = BH## Limma step 6/6: 2/2: Creating table: failure. Adjust = BH## The factor cure has 67 rows.## The factor failure has 56 rows.## plot labels was not set and there are more than 100 samples, disabling it.## Testing each factor against the others.## Scoring cure against everything else.## Scoring failure against everything else.## Deleting the file analyses/4_tumaco/GSVA/t_clinical_gsva_h.xlsx before writing the tables.3.1.2.4 Tumaco Biopsies c2
t_biopsy_gsva_c2 <- simple_gsva(
t_biopsies,
signatures=broad_c2,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
signature_category="c2")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 6353 rownames shared with the gsva result out of 6353.t_biopsy_gsva_c2_sig <- get_sig_gsva_categories(
t_biopsy_gsva_c2,
excel="analyses/4_tumaco/GSVA/t_biopsy_gsva_c2.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: Tumacofailure_vs_Tumacocure. Adjust = BH## Limma step 6/6: 1/2: Creating table: Tumacocure. Adjust = BH## Limma step 6/6: 2/2: Creating table: Tumacofailure. Adjust = BH## The factor Tumaco_cure has 9 rows.## The factor Tumaco_failure has 5 rows.## Testing each factor against the others.## Scoring Tumaco_cure against everything else.## Scoring Tumaco_failure against everything else.## Deleting the file analyses/4_tumaco/GSVA/t_biopsy_gsva_c2.xlsx before writing the tables.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : t,NUFIP1,26747|2 ... x_at,EEF1A1,1915 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2|39449_at,,|355 ... 14_at,UBA2,10054 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : NUP42,11097|1654 ... 4_at,UBE2D3,7323 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 203395_s_at,HES1 ... 4_s_at,CTBS,1486 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ENSG00000273641, ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 16224|Arid4b,ARI ... gcs1,HMGCS1,3157 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 643180|218637_at ... 0_s_at,NREP,9315 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ,51283|1442393_a ... 11_s_at,DBP,1628 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 343|ENSG00000182 ... 499,FAM20C,56975 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |219698_s_at,MET ... _at,TMEM97,27346 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 7|ENSG0000019736 ... 000288631,162699 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2804,KRTAP10-7,3 ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 701_s_at,CHCHD7, ... 0_at,SH2B3,10019 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 101927051|204365 ... _at,EPS8L2,64787 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |rc_AA957218_at, ... 8|rc_H33093_at,, is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 824,HDGFL1,15415 ... 7495,TMED3,23423 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : L2,27039|8108287 ... 7,CCDC187,399693 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : NUP42,11097|1654 ... 4_at,UBE2D3,7323 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 203395_s_at,HES1 ... 4_s_at,CTBS,1486 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2|39449_at,,|355 ... 14_at,UBA2,10054 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : t,NUFIP1,26747|2 ... x_at,EEF1A1,1915 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ENSG00000273641, ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 16224|Arid4b,ARI ... gcs1,HMGCS1,3157 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 643180|218637_at ... 0_s_at,NREP,9315 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |219698_s_at,MET ... _at,TMEM97,27346 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 343|ENSG00000182 ... 499,FAM20C,56975 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ,51283|1442393_a ... 11_s_at,DBP,1628 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 7|ENSG0000019736 ... 000288631,162699 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2804,KRTAP10-7,3 ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 701_s_at,CHCHD7, ... 0_at,SH2B3,10019 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 101927051|204365 ... _at,EPS8L2,64787 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |rc_AA957218_at, ... 8|rc_H33093_at,, is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 824,HDGFL1,15415 ... 7495,TMED3,23423 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : L2,27039|8108287 ... 7,CCDC187,399693 is truncated.
## Number of characters exeed the limit of 32767.3.1.2.5 Tumaco Biopsies c7
t_biopsy_gsva_c7 <- simple_gsva(
t_biopsies,
signatures=broad_c7,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
signature_category="c7")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 5209 rownames shared with the gsva result out of 5209.t_biopsy_gsva_c7_sig <- get_sig_gsva_categories(
t_biopsy_gsva_c7,
excel="analyses/4_tumaco/GSVA/t_biopsy_gsva_c7.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: Tumacofailure_vs_Tumacocure. Adjust = BH## Limma step 6/6: 1/2: Creating table: Tumacocure. Adjust = BH## Limma step 6/6: 2/2: Creating table: Tumacofailure. Adjust = BH## The factor Tumaco_cure has 9 rows.## The factor Tumaco_failure has 5 rows.## Testing each factor against the others.## Scoring Tumaco_cure against everything else.## Scoring Tumaco_failure against everything else.## Deleting the file analyses/4_tumaco/GSVA/t_biopsy_gsva_c7.xlsx before writing the tables.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 0750246|PRDM5,PR ... 9|OAS1,OAS1,4938 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 84296|PLEKHA1,PL ... 20H1,KMT5B,51111 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 0750246|PRDM5,PR ... 9|OAS1,OAS1,4938 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 84296|PLEKHA1,PL ... 20H1,KMT5B,51111 is truncated.
## Number of characters exeed the limit of 32767.3.1.2.6 Tumaco biopsies H
t_biopsy_gsva_h <- simple_gsva(
t_biopsies,
signatures=broad_h,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
signature_category="h")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 50 rownames shared with the gsva result out of 50.t_biopsy_gsva_h_sig <- get_sig_gsva_categories(
t_biopsy_gsva_h,
excel="analyses/4_tumaco/GSVA/t_biopsy_gsva_h.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: Tumacofailure_vs_Tumacocure. Adjust = BH## Limma step 6/6: 1/2: Creating table: Tumacocure. Adjust = BH## Limma step 6/6: 2/2: Creating table: Tumacofailure. Adjust = BH## The factor Tumaco_cure has 9 rows.## The factor Tumaco_failure has 5 rows.## Testing each factor against the others.## Scoring Tumaco_cure against everything else.## Scoring Tumaco_failure against everything else.## Deleting the file analyses/4_tumaco/GSVA/t_biopsy_gsva_h.xlsx before writing the tables.3.1.2.7 Tumaco Eosinophils C7
t_eosinophil_gsva_c7 <- simple_gsva(
t_eosinophils,
signatures=broad_c7,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
signature_category="c7")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 5209 rownames shared with the gsva result out of 5209.t_eosinophil_gsva_c7_sig <- get_sig_gsva_categories(
t_eosinophil_gsva_c7,
excel="analyses/4_tumaco/GSVA/t_eosinophil_gsva_c7.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: Tumacofailure_vs_Tumacocure. Adjust = BH## Limma step 6/6: 1/2: Creating table: Tumacocure. Adjust = BH## Limma step 6/6: 2/2: Creating table: Tumacofailure. Adjust = BH## The factor Tumaco_cure has 17 rows.## The factor Tumaco_failure has 9 rows.## Testing each factor against the others.## Scoring Tumaco_cure against everything else.## Scoring Tumaco_failure against everything else.## Deleting the file analyses/4_tumaco/GSVA/t_eosinophil_gsva_c7.xlsx before writing the tables.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 0750246|PRDM5,PR ... 9|OAS1,OAS1,4938 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 84296|PLEKHA1,PL ... 20H1,KMT5B,51111 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 0750246|PRDM5,PR ... 9|OAS1,OAS1,4938 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 84296|PLEKHA1,PL ... 20H1,KMT5B,51111 is truncated.
## Number of characters exeed the limit of 32767.3.1.2.8 Tumaco Eosinophils C2
t_eosinophil_gsva_c2 <- simple_gsva(
t_eosinophils,
signatures=broad_c2,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
signature_category="c2")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 6353 rownames shared with the gsva result out of 6353.t_eosinophil_gsva_c2_sig <- get_sig_gsva_categories(
t_eosinophil_gsva_c2,
excel="analyses/4_tumaco/GSVA/t_eosinophil_gsva_c2.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: Tumacofailure_vs_Tumacocure. Adjust = BH## Limma step 6/6: 1/2: Creating table: Tumacocure. Adjust = BH## Limma step 6/6: 2/2: Creating table: Tumacofailure. Adjust = BH## The factor Tumaco_cure has 17 rows.## The factor Tumaco_failure has 9 rows.## Testing each factor against the others.## Scoring Tumaco_cure against everything else.## Scoring Tumaco_failure against everything else.## Deleting the file analyses/4_tumaco/GSVA/t_eosinophil_gsva_c2.xlsx before writing the tables.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2|39449_at,,|355 ... 14_at,UBA2,10054 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : NUP42,11097|1654 ... 4_at,UBE2D3,7323 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : t,NUFIP1,26747|2 ... x_at,EEF1A1,1915 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 16224|Arid4b,ARI ... gcs1,HMGCS1,3157 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ENSG00000273641, ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 203395_s_at,HES1 ... 4_s_at,CTBS,1486 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 343|ENSG00000182 ... 499,FAM20C,56975 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 7|ENSG0000019736 ... 000288631,162699 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |219698_s_at,MET ... _at,TMEM97,27346 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ,51283|1442393_a ... 11_s_at,DBP,1628 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 643180|218637_at ... 0_s_at,NREP,9315 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 701_s_at,CHCHD7, ... 0_at,SH2B3,10019 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2804,KRTAP10-7,3 ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 101927051|204365 ... _at,EPS8L2,64787 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |rc_AA957218_at, ... 8|rc_H33093_at,, is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 824,HDGFL1,15415 ... 7495,TMED3,23423 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : L2,27039|8108287 ... 7,CCDC187,399693 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2|39449_at,,|355 ... 14_at,UBA2,10054 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : NUP42,11097|1654 ... 4_at,UBE2D3,7323 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : t,NUFIP1,26747|2 ... x_at,EEF1A1,1915 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ENSG00000273641, ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 16224|Arid4b,ARI ... gcs1,HMGCS1,3157 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 203395_s_at,HES1 ... 4_s_at,CTBS,1486 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 343|ENSG00000182 ... 499,FAM20C,56975 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 7|ENSG0000019736 ... 000288631,162699 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |219698_s_at,MET ... _at,TMEM97,27346 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ,51283|1442393_a ... 11_s_at,DBP,1628 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 643180|218637_at ... 0_s_at,NREP,9315 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 701_s_at,CHCHD7, ... 0_at,SH2B3,10019 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2804,KRTAP10-7,3 ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 101927051|204365 ... _at,EPS8L2,64787 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |rc_AA957218_at, ... 8|rc_H33093_at,, is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 824,HDGFL1,15415 ... 7495,TMED3,23423 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : L2,27039|8108287 ... 7,CCDC187,399693 is truncated.
## Number of characters exeed the limit of 32767.3.1.2.9 Tumaco Eosinophils H
t_eosinophil_gsva_h <- simple_gsva(
t_eosinophils,
signatures=broad_h,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
signature_category="h")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 50 rownames shared with the gsva result out of 50.t_eosinophil_gsva_h_sig <- get_sig_gsva_categories(
t_eosinophil_gsva_h,
excel="analyses/4_tumaco/GSVA/t_eosinophil_gsva_h.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: Tumacofailure_vs_Tumacocure. Adjust = BH## Limma step 6/6: 1/2: Creating table: Tumacocure. Adjust = BH## Limma step 6/6: 2/2: Creating table: Tumacofailure. Adjust = BH## The factor Tumaco_cure has 17 rows.## The factor Tumaco_failure has 9 rows.## Testing each factor against the others.## Scoring Tumaco_cure against everything else.## Scoring Tumaco_failure against everything else.## Deleting the file analyses/4_tumaco/GSVA/t_eosinophil_gsva_h.xlsx before writing the tables.3.1.2.10 Tumaco Monocytes C7
t_monocyte_gsva_c7 <- simple_gsva(
t_monocytes,
signatures=broad_c7,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
signature_category="c7")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 5209 rownames shared with the gsva result out of 5209.t_monocyte_gsva_c7_sig <- get_sig_gsva_categories(
t_monocyte_gsva_c7,
excel="analyses/4_tumaco/GSVA/t_monocyte_gsva_c7.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: Tumacofailure_vs_Tumacocure. Adjust = BH## Limma step 6/6: 1/2: Creating table: Tumacocure. Adjust = BH## Limma step 6/6: 2/2: Creating table: Tumacofailure. Adjust = BH## The factor Tumaco_cure has 21 rows.## The factor Tumaco_failure has 21 rows.## Testing each factor against the others.## Scoring Tumaco_cure against everything else.## Scoring Tumaco_failure against everything else.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 0750246|PRDM5,PR ... 9|OAS1,OAS1,4938 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 84296|PLEKHA1,PL ... 20H1,KMT5B,51111 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 0750246|PRDM5,PR ... 9|OAS1,OAS1,4938 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 84296|PLEKHA1,PL ... 20H1,KMT5B,51111 is truncated.
## Number of characters exeed the limit of 32767.3.1.2.11 Tumaco Monocytes C2
t_monocyte_gsva_c2 <- simple_gsva(
t_monocytes,
signatures=broad_c2,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
signature_category="c2")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 6353 rownames shared with the gsva result out of 6353.t_monocyte_gsva_c2_sig <- get_sig_gsva_categories(
t_monocyte_gsva_c2,
excel="analyses/4_tumaco/GSVA/t_monocyte_gsva_c2.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: Tumacofailure_vs_Tumacocure. Adjust = BH## Limma step 6/6: 1/2: Creating table: Tumacocure. Adjust = BH## Limma step 6/6: 2/2: Creating table: Tumacofailure. Adjust = BH## The factor Tumaco_cure has 21 rows.## The factor Tumaco_failure has 21 rows.## Testing each factor against the others.## Scoring Tumaco_cure against everything else.## Scoring Tumaco_failure against everything else.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2|39449_at,,|355 ... 14_at,UBA2,10054 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : NUP42,11097|1654 ... 4_at,UBE2D3,7323 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ENSG00000273641, ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : t,NUFIP1,26747|2 ... x_at,EEF1A1,1915 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 16224|Arid4b,ARI ... gcs1,HMGCS1,3157 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 203395_s_at,HES1 ... 4_s_at,CTBS,1486 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 643180|218637_at ... 0_s_at,NREP,9315 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 343|ENSG00000182 ... 499,FAM20C,56975 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |219698_s_at,MET ... _at,TMEM97,27346 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ,51283|1442393_a ... 11_s_at,DBP,1628 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 7|ENSG0000019736 ... 000288631,162699 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 701_s_at,CHCHD7, ... 0_at,SH2B3,10019 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2804,KRTAP10-7,3 ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 101927051|204365 ... _at,EPS8L2,64787 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |rc_AA957218_at, ... 8|rc_H33093_at,, is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 824,HDGFL1,15415 ... 7495,TMED3,23423 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : L2,27039|8108287 ... 7,CCDC187,399693 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2|39449_at,,|355 ... 14_at,UBA2,10054 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ENSG00000273641, ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : NUP42,11097|1654 ... 4_at,UBE2D3,7323 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : t,NUFIP1,26747|2 ... x_at,EEF1A1,1915 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 16224|Arid4b,ARI ... gcs1,HMGCS1,3157 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 203395_s_at,HES1 ... 4_s_at,CTBS,1486 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 643180|218637_at ... 0_s_at,NREP,9315 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 343|ENSG00000182 ... 499,FAM20C,56975 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ,51283|1442393_a ... 11_s_at,DBP,1628 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |219698_s_at,MET ... _at,TMEM97,27346 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 7|ENSG0000019736 ... 000288631,162699 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 701_s_at,CHCHD7, ... 0_at,SH2B3,10019 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2804,KRTAP10-7,3 ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 101927051|204365 ... _at,EPS8L2,64787 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |rc_AA957218_at, ... 8|rc_H33093_at,, is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 824,HDGFL1,15415 ... 7495,TMED3,23423 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : L2,27039|8108287 ... 7,CCDC187,399693 is truncated.
## Number of characters exeed the limit of 32767.3.1.2.12 Tumaco Monocytes H
t_monocyte_gsva_h <- simple_gsva(
t_monocytes,
signatures=broad_h,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
signature_category="h")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 50 rownames shared with the gsva result out of 50.t_monocyte_gsva_h_sig <- get_sig_gsva_categories(
t_monocyte_gsva_h,
excel="analyses/4_tumaco/GSVA/t_monocyte_gsva_h.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: Tumacofailure_vs_Tumacocure. Adjust = BH## Limma step 6/6: 1/2: Creating table: Tumacocure. Adjust = BH## Limma step 6/6: 2/2: Creating table: Tumacofailure. Adjust = BH## The factor Tumaco_cure has 21 rows.## The factor Tumaco_failure has 21 rows.## Testing each factor against the others.## Scoring Tumaco_cure against everything else.## Scoring Tumaco_failure against everything else.3.1.2.13 Tumaco Neutrophils c7
t_neutrophil_gsva_c7 <- simple_gsva(
t_neutrophils,
signatures=broad_c7,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
signature_category="c7")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 5209 rownames shared with the gsva result out of 5209.t_neutrophil_gsva_c7_sig <- get_sig_gsva_categories(
t_neutrophil_gsva_c7,
excel="analyses/4_tumaco/GSVA/t_neutrophil_gsva_c7.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: Tumacofailure_vs_Tumacocure. Adjust = BH## Limma step 6/6: 1/2: Creating table: Tumacocure. Adjust = BH## Limma step 6/6: 2/2: Creating table: Tumacofailure. Adjust = BH## The factor Tumaco_cure has 20 rows.## The factor Tumaco_failure has 21 rows.## Testing each factor against the others.## Scoring Tumaco_cure against everything else.## Scoring Tumaco_failure against everything else.## Deleting the file analyses/4_tumaco/GSVA/t_neutrophil_gsva_c7.xlsx before writing the tables.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 0750246|PRDM5,PR ... 9|OAS1,OAS1,4938 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 84296|PLEKHA1,PL ... 20H1,KMT5B,51111 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 0750246|PRDM5,PR ... 9|OAS1,OAS1,4938 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 84296|PLEKHA1,PL ... 20H1,KMT5B,51111 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 0750246|PRDM5,PR ... 9|OAS1,OAS1,4938 is truncated.
## Number of characters exeed the limit of 32767.3.1.2.14 Tumaco Neutrophils c2
t_neutrophil_gsva_c2 <- simple_gsva(
t_neutrophils,
signatures=broad_c2,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
signature_category="c2")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 6353 rownames shared with the gsva result out of 6353.t_neutrophil_gsva_c2_sig <- get_sig_gsva_categories(
t_neutrophil_gsva_c2,
excel="analyses/4_tumaco/GSVA/t_neutrophil_gsva_c2.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: Tumacofailure_vs_Tumacocure. Adjust = BH## Limma step 6/6: 1/2: Creating table: Tumacocure. Adjust = BH## Limma step 6/6: 2/2: Creating table: Tumacofailure. Adjust = BH## The factor Tumaco_cure has 20 rows.## The factor Tumaco_failure has 21 rows.## Testing each factor against the others.## Scoring Tumaco_cure against everything else.## Scoring Tumaco_failure against everything else.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ENSG00000273641, ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2|39449_at,,|355 ... 14_at,UBA2,10054 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : t,NUFIP1,26747|2 ... x_at,EEF1A1,1915 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : NUP42,11097|1654 ... 4_at,UBE2D3,7323 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 203395_s_at,HES1 ... 4_s_at,CTBS,1486 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 16224|Arid4b,ARI ... gcs1,HMGCS1,3157 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 343|ENSG00000182 ... 499,FAM20C,56975 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ,51283|1442393_a ... 11_s_at,DBP,1628 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 7|ENSG0000019736 ... 000288631,162699 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |219698_s_at,MET ... _at,TMEM97,27346 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 643180|218637_at ... 0_s_at,NREP,9315 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 701_s_at,CHCHD7, ... 0_at,SH2B3,10019 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2804,KRTAP10-7,3 ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 101927051|204365 ... _at,EPS8L2,64787 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |rc_AA957218_at, ... 8|rc_H33093_at,, is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 824,HDGFL1,15415 ... 7495,TMED3,23423 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : L2,27039|8108287 ... 7,CCDC187,399693 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ENSG00000273641, ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2|39449_at,,|355 ... 14_at,UBA2,10054 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : t,NUFIP1,26747|2 ... x_at,EEF1A1,1915 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : NUP42,11097|1654 ... 4_at,UBE2D3,7323 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 203395_s_at,HES1 ... 4_s_at,CTBS,1486 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 16224|Arid4b,ARI ... gcs1,HMGCS1,3157 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 343|ENSG00000182 ... 499,FAM20C,56975 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : ,51283|1442393_a ... 11_s_at,DBP,1628 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 7|ENSG0000019736 ... 000288631,162699 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |219698_s_at,MET ... _at,TMEM97,27346 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 643180|218637_at ... 0_s_at,NREP,9315 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 701_s_at,CHCHD7, ... 0_at,SH2B3,10019 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 2804,KRTAP10-7,3 ... 8516,PRKACA,5566 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 101927051|204365 ... _at,EPS8L2,64787 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : |rc_AA957218_at, ... 8|rc_H33093_at,, is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : 824,HDGFL1,15415 ... 7495,TMED3,23423 is truncated.
## Number of characters exeed the limit of 32767.## Warning in wb$writeData(df = x, colNames = TRUE, sheet = sheet, startRow = startRow, : L2,27039|8108287 ... 7,CCDC187,399693 is truncated.
## Number of characters exeed the limit of 32767.3.1.2.15 Tumaco Neutrophils H
t_neutrophil_gsva_h <- simple_gsva(
t_neutrophils,
signatures=broad_h,
msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
signature_category="h")## Converting the rownames() of the expressionset to ENTREZID.## 526 ENSEMBL ID's didn't have a matching ENTEREZ ID. Dropping them now.## Before conversion, the expressionset has 19923 entries.## After conversion, the expressionset has 19549 entries.## Adding annotations from reference/msigdb/msigdb_v7.5.1.xml.## Not subsetting the msigdb metadata, the wanted_meta argument was 'all'.## The downloaded msigdb contained 50 rownames shared with the gsva result out of 50.t_neutrophil_gsva_h_sig <- get_sig_gsva_categories(
t_neutrophil_gsva_h,
excel="analyses/4_tumaco/GSVA/t_neutrophil_gsva_h.xlsx")## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Assuming this data is similar to a micro array and not performign voom.## Limma step 3/6: running lmFit with method: ls.## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust = FALSE and trend = FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/1: Creating table: Tumacofailure_vs_Tumacocure. Adjust = BH## Limma step 6/6: 1/2: Creating table: Tumacocure. Adjust = BH## Limma step 6/6: 2/2: Creating table: Tumacofailure. Adjust = BH## The factor Tumaco_cure has 20 rows.## The factor Tumaco_failure has 21 rows.## Testing each factor against the others.## Scoring Tumaco_cure against everything else.## Scoring Tumaco_failure against everything else.if (!isTRUE(get0("skip_load"))) {
pander::pander(sessionInfo())
message(paste0("This is hpgltools commit: ", get_git_commit()))
message(paste0("Saving to ", savefile))
tmp <- sm(saveme(filename=savefile))
}tmp <- loadme(filename=savefile)---
title: "L. panamensis 202209: Likelihood Ratio Tests and GSVA"
author: "atb abelew@gmail.com"
date: "`r Sys.Date()`"
output:
  html_document:
    code_download: true
    code_folding: show
    fig_caption: true
    fig_height: 7
    fig_width: 7
    highlight: default
    keep_md: false
    mode: selfcontained
    number_sections: true
    self_contained: true
    theme: readable
    toc: true
    toc_float:
      collapsed: false
      smooth_scroll: false
---

<style>
body .main-container {
max-width: 1600px;
}
</style>

```{r options, include=FALSE}
library(hpgltools)
library(dplyr)
library(forcats)
tt <- sm(devtools::load_all("~/hpgltools"))
knitr::opts_knit$set(progress=TRUE,
                     verbose=TRUE,
                     width=90,
                     echo=TRUE)
knitr::opts_chunk$set(error=TRUE,
                      fig.width=8,
                      fig.height=8,
                      dpi=96)
old_options <- options(digits=4,
                       stringsAsFactors=FALSE,
                       knitr.duplicate.label="allow")
ggplot2::theme_set(ggplot2::theme_bw(base_size=12))
ver <- "202209"
previous_file <- ""
rundate <- format(Sys.Date(), format="%Y%m%d")

##tmp <- try(sm(loadme(filename=gsub(pattern="\\.Rmd", replace="\\.rda\\.xz", x=previous_file))))
rmd_file <- glue::glue("tmrc3_lrt_gsva_{ver}.Rmd")
savefile <- gsub(pattern="\\.Rmd", replace="\\.rda\\.xz", x=rmd_file)
loaded <- load(file=glue::glue("rda/tmrc3_data_structures-v{ver}.rda"))
```

# Introduction

Though there is no fundamental reason to separate the likelihood ratio
testing and GSVA from the differential expression analyses, they are
both tasks which reach back to the primary expression data, unlike
GSEA.  Therefore I chose to separate these two tasks into a their own
document.

# LRT

The likelihood ratio testing performed on the TMRC3 data is intended
to look for shared patterns of expression across some known, constant
factor.  This may be time (are there patterns across the visits of
each person), or cell type (do some genes act consistently across
type).  We could also ask this question of our two clinics, or indeed
across the cure/fail samples.

## Patterns across clinic

```{r lrt_clinics}
tc_clinical_filt <- normalize_expt(tc_clinical, filter = TRUE)

tc_lrt_clinic <- deseq_lrt(tc_clinical_filt, transform = "vst", interaction = FALSE,
                           interactor_column = "visitnumber",
                           interest_column = "clinic")
summary(lrt_visit[["favorite_genes"]])
```

```{r lrt_visit}
t_clinical_filt <- normalize_expt(t_clinical, filter=TRUE)

lrt_visit <- deseq_lrt(t_clinical_filt, transform = "vst", interaction = FALSE,
                       interactor_column = "visitnumber",
                       interest_column = "finaloutcome")
summary(lrt_visit[["favorite_genes"]])
written <- write_xlsx(data = as.data.frame(lrt_visit[["deseq_table"]]),
                      excel = glue::glue("excel/lrt_clinical_visit-v{ver}.xlsx"))

lrt_monocyte_visit <- deseq_lrt(t_visitcf_monocyte, transform = "vst",
                                interaction = FALSE,
                                interactor_column = "visitnumber",
                                interest_column = "finaloutcome")
lrt_monocyte_visit$cluster_data$plot

lrt_monocyte_visit_v2 <- deseq_lrt(t_visitcf_monocyte, transform = "vst",
                                   interaction = FALSE, minc = 1,
                                   interactor_column = "visitnumber",
                                   interest_column = "finaloutcome")
```

## Shared patterns across cell types

```{r lrt_celltype}
lrt_celltype_clinical_test <- deseq_lrt(tc_clinical, transform = "vst",
                                        interactor_column = "typeofcells",
                                        interest_column = "finaloutcome")

hs_annot <- fData(hs_expt)
deseq_lrt_df <- merge(hs_annot, as.data.frame(lrt_celltype_clinical_test[["deseq_table"]]), all.y=TRUE,
                      by="row.names")
rownames(deseq_lrt_df) <- deseq_lrt_df[["Row.names"]]
deseq_lrt_df[["Row.names"]] <- NULL
written <- write_xlsx(data=deseq_lrt_df,
                      excel=glue::glue("excel/lrt_clinical_celltype-v{ver}.xlsx"))
```

# GSVA

## Load some signatures

If one chooses, simple_gsva() can either load signatures from the
GSVAdata package, which is a little old, or load an arbitrary set.
load_gmt_signatures() provides a quick way to extract them from a gmt
file.


```{r load_signatures}
broad_c7 <- load_gmt_signatures(signatures="reference/msigdb/c7.all.v7.5.1.entrez.gmt",
                                signature_category="c7")
broad_c2 <- load_gmt_signatures(signatures="reference/msigdb/c2.all.v7.5.1.entrez.gmt",
                                signature_category="c2")
broad_h <- load_gmt_signatures(signatures="reference/msigdb/h.all.v7.5.1.entrez.gmt",
                               signature_category="h")
```

### Clinical samples

#### Clinical C2

```{r gsva, fig.show="hide"}
tc_celltype_gsva_c2 <- simple_gsva(
    tc_valid, signatures=broad_c2,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml")
tc_celltype_gsva_c2_sig <- get_sig_gsva_categories(
    tc_celltype_gsva_c2,
    excel="analyses/3_cali_and_tumaco/GSVA/tc_valid_gsva_c2.xlsx")
tc_celltype_gsva_c2_sig$subset_plot
tc_celltype_gsva_c2_sig$score_plot
```

#### Valid  C7

```{r gsva_valid_c7}
tc_celltype_gsva_c7 <- simple_gsva(
    tc_valid, signatures=broad_c7,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
    signature_category="c7")
tc_celltype_gsva_c7_sig <- get_sig_gsva_categories(
    tc_celltype_gsva_c7,
    excel="analyses/3_cali_and_tumaco/GSVA/tc_valid_gsva_c7.xlsx")
```

#### Valid H

```{r gsva_valid_h}
tc_celltype_gsva_h <- simple_gsva(
    tc_valid,
    signatures=broad_h,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
    signature_category="h")
tc_celltype_gsva_h_sig <- get_sig_gsva_categories(
    tc_celltype_gsva_h,
    excel="analyses/3_cali_and_tumaco/GSVA/tc_valid_gsva_h.xlsx")
```

### Tumaco samples

#### Clinical C2

```{r gsva_tumaco_clinical_c2}
t_clinical_gsva_c2 <- simple_gsva(
    t_clinical,
    signatures=broad_c2,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
    signature_category="c2")
t_clinical_gsva_c2_sig <- get_sig_gsva_categories(
    t_clinical_gsva_c2,
    excel="analyses/4_tumaco/GSVA/t_clinical_gsva_c2.xlsx")
t_clinical_gsva_c2_sig$subset_plot
t_clinical_gsva_c2_sig$score_plot
```

#### Clinical C7

```{r t_gsva_clinical_c7}
t_clinical_gsva_c7 <- simple_gsva(
    t_clinical,
    signatures=broad_c7,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
    signature_category="c7")
t_clinical_gsva_c7_sig <- get_sig_gsva_categories(
    t_clinical_gsva_c7,
    excel="analyses/4_tumaco/GSVA/t_clinical_gsva_c7.xlsx")
```

#### Clinical H

```{r t_clinical_gsva_h}
t_clinical_gsva_h <- simple_gsva(
    t_clinical,
    signatures=broad_h,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
    signature_category="h")
t_clinical_gsva_h_sig <- get_sig_gsva_categories(
    t_clinical_gsva_h,
    excel="analyses/4_tumaco/GSVA/t_clinical_gsva_h.xlsx")
```

#### Tumaco Biopsies c2

```{r gsva_tumaco_biopsy_c2}
t_biopsy_gsva_c2 <- simple_gsva(
    t_biopsies,
    signatures=broad_c2,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
    signature_category="c2")
t_biopsy_gsva_c2_sig <- get_sig_gsva_categories(
    t_biopsy_gsva_c2,
    excel="analyses/4_tumaco/GSVA/t_biopsy_gsva_c2.xlsx")
```

#### Tumaco Biopsies c7

```{r gsva_tumaco_biopsy_c7}
t_biopsy_gsva_c7 <- simple_gsva(
    t_biopsies,
    signatures=broad_c7,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
    signature_category="c7")
t_biopsy_gsva_c7_sig <- get_sig_gsva_categories(
    t_biopsy_gsva_c7,
    excel="analyses/4_tumaco/GSVA/t_biopsy_gsva_c7.xlsx")
```

#### Tumaco biopsies H

```{r gsva_tumaco_biopsies_h}
t_biopsy_gsva_h <- simple_gsva(
    t_biopsies,
    signatures=broad_h,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
    signature_category="h")
t_biopsy_gsva_h_sig <- get_sig_gsva_categories(
    t_biopsy_gsva_h,
    excel="analyses/4_tumaco/GSVA/t_biopsy_gsva_h.xlsx")
```

#### Tumaco Eosinophils C7

```{r gsva_tumaco_eosinophil_c7}
t_eosinophil_gsva_c7 <- simple_gsva(
    t_eosinophils,
    signatures=broad_c7,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
    signature_category="c7")
t_eosinophil_gsva_c7_sig <- get_sig_gsva_categories(
    t_eosinophil_gsva_c7,
    excel="analyses/4_tumaco/GSVA/t_eosinophil_gsva_c7.xlsx")
```

#### Tumaco Eosinophils C2

```{r gsva_tumaco_eosinophil_c2}
t_eosinophil_gsva_c2 <- simple_gsva(
    t_eosinophils,
    signatures=broad_c2,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
    signature_category="c2")
t_eosinophil_gsva_c2_sig <- get_sig_gsva_categories(
    t_eosinophil_gsva_c2,
    excel="analyses/4_tumaco/GSVA/t_eosinophil_gsva_c2.xlsx")
```

#### Tumaco Eosinophils H

```{r gsva_tumaco_eosinophil_h}
t_eosinophil_gsva_h <- simple_gsva(
    t_eosinophils,
    signatures=broad_h,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
    signature_category="h")
t_eosinophil_gsva_h_sig <- get_sig_gsva_categories(
    t_eosinophil_gsva_h,
    excel="analyses/4_tumaco/GSVA/t_eosinophil_gsva_h.xlsx")
```

#### Tumaco Monocytes C7

```{r gsva_tumaco_monocyte_c7}
t_monocyte_gsva_c7 <- simple_gsva(
    t_monocytes,
    signatures=broad_c7,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
    signature_category="c7")
t_monocyte_gsva_c7_sig <- get_sig_gsva_categories(
    t_monocyte_gsva_c7,
    excel="analyses/4_tumaco/GSVA/t_monocyte_gsva_c7.xlsx")
```

#### Tumaco Monocytes C2

```{r gsva_tumaco_monocyte_c2}
t_monocyte_gsva_c2 <- simple_gsva(
    t_monocytes,
    signatures=broad_c2,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
    signature_category="c2")
t_monocyte_gsva_c2_sig <- get_sig_gsva_categories(
    t_monocyte_gsva_c2,
    excel="analyses/4_tumaco/GSVA/t_monocyte_gsva_c2.xlsx")
```

#### Tumaco Monocytes H

```{r gsva_monocyte_tumaco_h}
t_monocyte_gsva_h <- simple_gsva(
    t_monocytes,
    signatures=broad_h,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
    signature_category="h")
t_monocyte_gsva_h_sig <- get_sig_gsva_categories(
    t_monocyte_gsva_h,
    excel="analyses/4_tumaco/GSVA/t_monocyte_gsva_h.xlsx")
```

#### Tumaco Neutrophils c7

```{r gsva_neutrophils_tumaco_c7}
t_neutrophil_gsva_c7 <- simple_gsva(
    t_neutrophils,
    signatures=broad_c7,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
    signature_category="c7")
t_neutrophil_gsva_c7_sig <- get_sig_gsva_categories(
    t_neutrophil_gsva_c7,
    excel="analyses/4_tumaco/GSVA/t_neutrophil_gsva_c7.xlsx")
```

#### Tumaco Neutrophils c2

```{r gsva_tumaco_neutrophil_c2}
t_neutrophil_gsva_c2 <- simple_gsva(
    t_neutrophils,
    signatures=broad_c2,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
    signature_category="c2")
t_neutrophil_gsva_c2_sig <- get_sig_gsva_categories(
    t_neutrophil_gsva_c2,
    excel="analyses/4_tumaco/GSVA/t_neutrophil_gsva_c2.xlsx")
```

#### Tumaco Neutrophils H

```{r tumaco_gsva_neutrophil_h}
t_neutrophil_gsva_h <- simple_gsva(
    t_neutrophils,
    signatures=broad_h,
    msig_xml="reference/msigdb/msigdb_v7.5.1.xml",
    signature_category="h")
t_neutrophil_gsva_h_sig <- get_sig_gsva_categories(
    t_neutrophil_gsva_h,
    excel="analyses/4_tumaco/GSVA/t_neutrophil_gsva_h.xlsx")
```

```{r saveme, eval=FALSE}
if (!isTRUE(get0("skip_load"))) {
  pander::pander(sessionInfo())
  message(paste0("This is hpgltools commit: ", get_git_commit()))
  message(paste0("Saving to ", savefile))
  tmp <- sm(saveme(filename=savefile))
}
```

```{r loadme_after, eval=FALSE}
tmp <- loadme(filename=savefile)
```
