We take the annotation data from ensembl’s biomart instance. The genome which was used to map the data was hg38 revision 91. My default when using biomart is to load the data from 1 year before the current date, which provides annotations which match hg38 91 almost perfectly.
hs_annot <- load_biomart_annotations(year="2020", month="jan")## The biomart annotations file already exists, loading from it.hs_annot <- hs_annot[["annotation"]]
hs_annot[["transcript"]] <- paste0(rownames(hs_annot), ".", hs_annot[["version"]])
rownames(hs_annot) <- make.names(hs_annot[["ensembl_gene_id"]], unique=TRUE)
tx_gene_map <- hs_annot[, c("transcript", "ensembl_gene_id")]I used two mapping methods for this data, hisat2 and salmon. Most analyses use hisat2, which is a more traditional map-and-count method. In contrast, salmon uses what may be thought of as a indexed voting method (so that multi-matches are discounted and the votes split among all matches). Salmon also required a pre-existing database of known transcripts (though later versions may actually use mapping from things like hisat), while hisat uses the genome and a database of known transcripts (and optionally can search for splicing junctions to find new transcripts).
The first thing to note is the large range in coverage. There are multiple samples with coverage which is too low to use. These will be removed shortly.
sanitize_columns <- c("donor", "drug", "condition", "batch", "macrophagetreatment",
"macrophageinfectionzymodeme")
macr <- create_expt("sample_sheets/tmrc2_macrophage_samples_202203.xlsx",
file_column = "hg38100hisatfile",
savefile = "hs_expt_all.rda",
gene_info = hs_annot) %>%
exclude_genes_expt(column = "gene_biotype", method = "keep",
pattern = "protein_coding") %>%
subset_expt(nonzero = 11000) %>%
set_expt_factors(columns = sanitize_columns) %>%
set_expt_factors(columns=sanitize_columns, class="factor") %>%
set_expt_batches(fact="macrophagetreatment") %>%
set_expt_conditions(fact="macrophageinfectionzymodeme")## Reading the sample metadata.## The sample definitions comprises: 28 rows(samples) and 67 columns(metadata fields).## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': error in evaluating the argument 'object' in selecting a method for function 'pData': error in evaluating the argument 'object' in selecting a method for function 'fData': error in evaluating the argument 'object' in selecting a method for function 'fData': error in evaluating the argument 'object' in selecting a method for function 'sampleNames': object 'filenames' not foundThese samples are rather different from all of the others. The following section is therefore written primarily in response to a separate set of emails from Olga and Maria Adelaida; here is a snippet:
Dear all, about the samples corresponding to infected macrophages with three sensitive (2.2) and three resistant (2.3) clinical strains of L. (V.) panamensis, I send you the results of parasite burden by detection of 7SLRNA. I think these results are interesting, but the sample size is very small. Doctor Najib or Trey could you please send me the quality data and PCA analysis of these samples?
and
Hi Doctor, thank you. These samples corresponding to primary macrophages infected with clinical strains 2.2 (n=3) and 2.3 (n = 3). These information is in the file: TMRC project 3: excel Host TMRC3 v1.1, rows 137 to 150.
Thus I added 3 columns to the end of the sample sheet which seek to include this information. The first is ‘drug’ and encodes both the infection state (no for the two controls and yes for everything else), the second is zymodeme which I took from the tmrc2 sample sheet, the last is drug, which is either no or sb.
table(pData(macr)[["condition"]])## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': object 'macr' not foundtable(pData(macr)[["batch"]])## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': object 'macr' not foundtable(pData(macr)[["macrophagetreatment"]])## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': object 'macr' not foundtable(pData(macr)[["macrophageinfectionzymodeme"]])## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': object 'macr' not foundmacr_libsize <- plot_libsize(macr, yscale=TRUE)## Error in h(simpleError(msg, call)): error in evaluating the argument 'data' in selecting a method for function 'plot_libsize': object 'macr' not foundpp(file="macrophage_side_experiment/macr_libsize.png", image=macr_libsize$plot)## Error in pp(file = "macrophage_side_experiment/macr_libsize.png", image = macr_libsize$plot): object 'macr_libsize' not foundmacr_nonzero <- plot_nonzero(macr)## Error in plot_nonzero(macr): object 'macr' not foundpp(file="macrophage_side_experiment/macr_nonzero.png", image=macr_nonzero$plot)## Error in pp(file = "macrophage_side_experiment/macr_nonzero.png", image = macr_nonzero$plot): object 'macr_nonzero' not foundmacr_norm <- sm(normalize_expt(macr, transform="log2", norm="quant", convert="cpm", filter=TRUE))## Error in normalize_expt(macr, transform = "log2", norm = "quant", convert = "cpm", : object 'macr' not foundnorm_pca <- plot_pca(macr_norm, plot_labels=FALSE)## Error in plot_pca(macr_norm, plot_labels = FALSE): object 'macr_norm' not foundnorm_pca$plot## Error in eval(expr, envir, enclos): object 'norm_pca' not foundpp(file="macrophage_side_experiment/pca_colors_zymodeme.png", image=norm_pca$plot)## Error in pp(file = "macrophage_side_experiment/pca_colors_zymodeme.png", : object 'norm_pca' not foundtreatment_macr <- set_expt_conditions(macr, fact="macrophagetreatment") %>%
set_expt_batches(fact="macrophageinfectionzymodeme")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': error in evaluating the argument 'object' in selecting a method for function 'pData': object 'macr' not foundtreatment_norm <- sm(normalize_expt(treatment_macr, transform="log2", norm="quant", convert="cpm", filter=TRUE))## Error in normalize_expt(treatment_macr, transform = "log2", norm = "quant", : object 'treatment_macr' not foundtreatment_pca <- plot_pca(treatment_norm, plot_labels=FALSE)## Error in plot_pca(treatment_norm, plot_labels = FALSE): object 'treatment_norm' not foundtreatment_pca$plot## Error in eval(expr, envir, enclos): object 'treatment_pca' not foundpp(file="macrophage_side_experiment/pca_colors_treatment.png", image=treatment_pca$plot)## Error in pp(file = "macrophage_side_experiment/pca_colors_treatment.png", : object 'treatment_pca' not foundplot_3d_pca(norm_pca)$plot## Error in plot_3d_pca(norm_pca): object 'norm_pca' not foundmacr_nb <- sm(normalize_expt(macr, norm = "quant", convert = "cpm",
transform = "log2", batch = "svaseq", filter = TRUE))## Error in normalize_expt(macr, norm = "quant", convert = "cpm", transform = "log2", : object 'macr' not foundnb_pca <- plot_pca(macr_nb, plot_labels=FALSE)## Error in plot_pca(macr_nb, plot_labels = FALSE): object 'macr_nb' not foundpp(file="macrophage_side_experiment/normbatch_pca.png", image=nb_pca$plot)## Error in pp(file = "macrophage_side_experiment/normbatch_pca.png", image = nb_pca$plot): object 'nb_pca' not foundmacr_written <- sm(write_expt(macr, excel="macrophage_side_experiment/macrophage_expt.xlsx"))## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'exprs': object 'macr' not foundThere were a couple of contrasts explicitly requested for this data:
Unfortunately, I think to really answer these questions we will require more replicates of a few of these conditions, most notably the uninfected samples.
treatment_macr <- set_expt_conditions(macr, fact="macrophagetreatment") %>%
set_expt_batches(fact="macrophageinfectionzymodeme")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': error in evaluating the argument 'object' in selecting a method for function 'pData': object 'macr' not found##tmp <- normalize_expt(macr, filter=TRUE)
##zy_de <- deseq_pairwise(tmp, model_batch="svaseq")
##zy_ed <- edger_pairwise(tmp, model_batch="svaseq")
combined_condition <- paste0(pData(macr)[["macrophagetreatment"]], "_",
pData(macr)[["macrophageinfectionzymodeme"]])## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': object 'macr' not foundpData(macr[["expressionset"]])[["combined"]] <- combined_condition## Error in eval(expr, envir, enclos): object 'combined_condition' not foundmacr <- set_expt_conditions(macr, fact = "combined")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': object 'macr' not foundzymo_de <- all_pairwise(macr, model_batch = "svaseq", filter = TRUE,
do_ebseq = FALSE)## Error in normalize_expt(input, filter = filter): object 'macr' not foundkeepers <- list(
"z22_uninf" = c("infz22", "uninfnone"),
"z23_uninf" = c("infz23", "uninfnone"),
"z22_sbuninf" = c("infsbz22", "uninfsbnone"),
"z23_sbuninf" = c("infsbz23", "uninfsbnone"),
"zymo_nodrug" = c("infz23", "infz22"),
"z23_uninf" = c("infz23", "uninfnozymo"))
zymo_table <- combine_de_tables(
zymo_de, keepers=keepers,
excel="macrophage_side_experiment/macrophage_de.xlsx")## Deleting the file macrophage_side_experiment/macrophage_de.xlsx before writing the tables.## Error in combine_de_tables(zymo_de, keepers = keepers, excel = "macrophage_side_experiment/macrophage_de.xlsx"): object 'zymo_de' not foundpp(file="images/z22_vs_uninfected_ma.png", image=zymo_table$plots$z22_uninf$deseq_ma_plots$plot)## Error in pp(file = "images/z22_vs_uninfected_ma.png", image = zymo_table$plots$z22_uninf$deseq_ma_plots$plot): object 'zymo_table' not foundpp(file="images/z22_vs_sb_uninfected_ma.png", image=zymo_table$plots$z22_sbuninf$deseq_ma_plots$plot)## Error in pp(file = "images/z22_vs_sb_uninfected_ma.png", image = zymo_table$plots$z22_sbuninf$deseq_ma_plots$plot): object 'zymo_table' not foundpp(file="images/z23_vs_uninfected_ma.png", image=zymo_table$plots$z23_uninf$deseq_ma_plots$plot)## Error in pp(file = "images/z23_vs_uninfected_ma.png", image = zymo_table$plots$z23_uninf$deseq_ma_plots$plot): object 'zymo_table' not foundpp(file="images/z23_vs_sb_uninfected_ma.png", image=zymo_table$plots$z23_sbuninf$deseq_ma_plots$plot)## Error in pp(file = "images/z23_vs_sb_uninfected_ma.png", image = zymo_table$plots$z23_sbuninf$deseq_ma_plots$plot): object 'zymo_table' not foundzymo_sig <- extract_significant_genes(zymo_table, according_to="deseq")## Error in extract_significant_genes(zymo_table, according_to = "deseq"): object 'zymo_table' not foundz22_ma <- plot_ma_de(zymo_table[["data"]][["z22_uninf"]], expr_col="deseq_basemean",
fc_col="deseq_logfc", p_col="deseq_adjp")## Error in plot_ma_de(zymo_table[["data"]][["z22_uninf"]], expr_col = "deseq_basemean", : object 'zymo_table' not foundz22_ma$plot## Error in eval(expr, envir, enclos): object 'z22_ma' not foundz22_uninf_up_sig <- zymo_sig[["deseq"]][["ups"]][["z22_uninf"]]## Error in eval(expr, envir, enclos): object 'zymo_sig' not founddim(z22_uninf_up_sig)## Error in eval(expr, envir, enclos): object 'z22_uninf_up_sig' not foundz22_uninf_down_sig <- zymo_sig[["deseq"]][["downs"]][["z22_uninf"]]## Error in eval(expr, envir, enclos): object 'zymo_sig' not founddim(z22_uninf_down_sig)## Error in eval(expr, envir, enclos): object 'z22_uninf_down_sig' not foundz22_sbuninf_up_sig <- zymo_sig[["deseq"]][["ups"]][["z22_sbuninf"]]## Error in eval(expr, envir, enclos): object 'zymo_sig' not founddim(z22_sbuninf_up_sig)## Error in eval(expr, envir, enclos): object 'z22_sbuninf_up_sig' not foundz22_sbuninf_down_sig <- zymo_sig[["deseq"]][["downs"]][["z22_sbuninf"]]## Error in eval(expr, envir, enclos): object 'zymo_sig' not founddim(z22_sbuninf_down_sig)## Error in eval(expr, envir, enclos): object 'z22_sbuninf_down_sig' not foundz23_ma <- plot_ma_de(zymo_table[["data"]][["z23_uninf"]], expr_col="deseq_basemean",
fc_col="deseq_logfc", p_col="deseq_adjp")## Error in plot_ma_de(zymo_table[["data"]][["z23_uninf"]], expr_col = "deseq_basemean", : object 'zymo_table' not foundz23_ma$plot## Error in eval(expr, envir, enclos): object 'z23_ma' not foundz23_uninf_up_sig <- zymo_sig[["deseq"]][["ups"]][["z23_uninf"]]## Error in eval(expr, envir, enclos): object 'zymo_sig' not founddim(z23_uninf_up_sig)## Error in eval(expr, envir, enclos): object 'z23_uninf_up_sig' not foundz23_uninf_down_sig <- zymo_sig[["deseq"]][["downs"]][["z23_uninf"]]## Error in eval(expr, envir, enclos): object 'zymo_sig' not founddim(z23_uninf_down_sig)## Error in eval(expr, envir, enclos): object 'z23_uninf_down_sig' not foundz23_sbuninf_up_sig <- zymo_sig[["deseq"]][["ups"]][["z23_sbuninf"]]## Error in eval(expr, envir, enclos): object 'zymo_sig' not founddim(z23_sbuninf_up_sig)## Error in eval(expr, envir, enclos): object 'z23_sbuninf_up_sig' not foundz23_sbuninf_down_sig <- zymo_sig[["deseq"]][["downs"]][["z23_sbuninf"]]## Error in eval(expr, envir, enclos): object 'zymo_sig' not founddim(z23_sbuninf_down_sig)## Error in eval(expr, envir, enclos): object 'z23_sbuninf_down_sig' not foundz22_z23_nosb_groups <- list(
"z22_up" = rownames(z22_uninf_up_sig),
"z23_up" = rownames(z23_uninf_up_sig))## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'z22_uninf_up_sig' not foundz22_z23_nosb_venn <- Vennerable::Venn(Sets = z22_z23_nosb_groups)## Error in Vennerable::Venn(Sets = z22_z23_nosb_groups): object 'z22_z23_nosb_groups' not foundpp(file="images/z22_z23_nosb_venn.png")## NULLz22_z23_nosb_venn_plot <- Vennerable::plot(z22_z23_nosb_venn, doWeights = FALSE)## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'z22_z23_nosb_venn' not founddev.off()## png
## 2annot <- fData(macr)## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'fData': object 'macr' not foundz23_nosb_unique <- z22_z23_nosb_venn@IntersectionSets[["01"]]## Error in eval(expr, envir, enclos): object 'z22_z23_nosb_venn' not foundwanted <- rownames(annot) %in% z23_nosb_unique## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function '%in%': error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'annot' not foundz23_wanted <- annot[wanted, ]## Error in eval(expr, envir, enclos): object 'annot' not foundwritten <- write_xlsx(z23_wanted, excel="excel/z23_nosb_unique_genes.xlsx")## Error in write_xlsx(z23_wanted, excel = "excel/z23_nosb_unique_genes.xlsx"): object 'z23_wanted' not foundz22_nosb_unique <- z22_z23_nosb_venn@IntersectionSets[["10"]]## Error in eval(expr, envir, enclos): object 'z22_z23_nosb_venn' not foundwanted <- rownames(annot) %in% z22_nosb_unique## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function '%in%': error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'annot' not foundz22_wanted <- annot[wanted, ]## Error in eval(expr, envir, enclos): object 'annot' not foundwritten <- write_xlsx(z22_wanted, excel="excel/z22_nosb_unique_genes.xlsx")## Error in write_xlsx(z22_wanted, excel = "excel/z22_nosb_unique_genes.xlsx"): object 'z22_wanted' not foundz22_nosb_shared <- z22_z23_nosb_venn@IntersectionSets[["11"]]## Error in eval(expr, envir, enclos): object 'z22_z23_nosb_venn' not foundwanted <- rownames(annot) %in% z22_nosb_shared## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function '%in%': error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'annot' not foundshared_wanted <- annot[wanted, ]## Error in eval(expr, envir, enclos): object 'annot' not foundwritten <- write_xlsx(shared_wanted, excel="excel/z22_z23_nosb_shared_genes.xlsx")## Error in write_xlsx(shared_wanted, excel = "excel/z22_z23_nosb_shared_genes.xlsx"): object 'shared_wanted' not foundz22_unique_gp <- simple_gprofiler(rownames(z22_wanted))## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'z22_wanted' not foundpp(file="images/z22_unique_bp.png", image=z22_unique_gp[["pvalue_plots"]][["bpp_plot_over"]], height=9, width=6)## Error in pp(file = "images/z22_unique_bp.png", image = z22_unique_gp[["pvalue_plots"]][["bpp_plot_over"]], : object 'z22_unique_gp' not foundpp(file="images/z22_unique_kegg.png", image=z22_unique_gp[["pvalue_plots"]][["kegg_plot_over"]])## Error in pp(file = "images/z22_unique_kegg.png", image = z22_unique_gp[["pvalue_plots"]][["kegg_plot_over"]]): object 'z22_unique_gp' not foundpp(file="images/z22_unique_reac.png", image=z22_unique_gp[["pvalue_plots"]][["reactome_plot_over"]])## Error in pp(file = "images/z22_unique_reac.png", image = z22_unique_gp[["pvalue_plots"]][["reactome_plot_over"]]): object 'z22_unique_gp' not foundz23_unique_gp <- simple_gprofiler(rownames(z23_wanted))## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'z23_wanted' not foundpp(file="images/z23_unique_bp.png", image=z23_unique_gp[["pvalue_plots"]][["bpp_plot_over"]], height=9, width=6)## Error in pp(file = "images/z23_unique_bp.png", image = z23_unique_gp[["pvalue_plots"]][["bpp_plot_over"]], : object 'z23_unique_gp' not foundpp(file="images/z23_unique_kegg.png", image=z23_unique_gp[["pvalue_plots"]][["kegg_plot_over"]])## Error in pp(file = "images/z23_unique_kegg.png", image = z23_unique_gp[["pvalue_plots"]][["kegg_plot_over"]]): object 'z23_unique_gp' not foundpp(file="images/z23_unique_reac.png", image=z23_unique_gp[["pvalue_plots"]][["reactome_plot_over"]])## Error in pp(file = "images/z23_unique_reac.png", image = z23_unique_gp[["pvalue_plots"]][["reactome_plot_over"]]): object 'z23_unique_gp' not foundpp(file="images/z23_unique_tf.png", image=z23_unique_gp[["pvalue_plots"]][["tf_plot_over"]])## Error in pp(file = "images/z23_unique_tf.png", image = z23_unique_gp[["pvalue_plots"]][["tf_plot_over"]]): object 'z23_unique_gp' not foundz22_z23_shared_gp <- simple_gprofiler(rownames(shared_wanted))## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'shared_wanted' not foundpp(file="images/z23_shared_bp.png", image=z22_z23_shared_gp[["pvalue_plots"]][["bpp_plot_over"]], height=9, width=6)## Error in pp(file = "images/z23_shared_bp.png", image = z22_z23_shared_gp[["pvalue_plots"]][["bpp_plot_over"]], : object 'z22_z23_shared_gp' not foundpp(file="images/z23_shared_kegg.png", image=z22_z23_shared_gp[["pvalue_plots"]][["kegg_plot_over"]])## Error in pp(file = "images/z23_shared_kegg.png", image = z22_z23_shared_gp[["pvalue_plots"]][["kegg_plot_over"]]): object 'z22_z23_shared_gp' not foundpp(file="images/z23_shared_reac.png", image=z22_z23_shared_gp[["pvalue_plots"]][["reactome_plot_over"]])## Error in pp(file = "images/z23_shared_reac.png", image = z22_z23_shared_gp[["pvalue_plots"]][["reactome_plot_over"]]): object 'z22_z23_shared_gp' not foundpp(file="images/z23_shared_tf.png", image=z22_z23_shared_gp[["pvalue_plots"]][["tf_plot_over"]])## Error in pp(file = "images/z23_shared_tf.png", image = z22_z23_shared_gp[["pvalue_plots"]][["tf_plot_over"]]): object 'z22_z23_shared_gp' not foundz22_uninf_up_gp <- simple_gprofiler(z22_uninf_up_sig)## Error in simple_gprofiler(z22_uninf_up_sig): object 'z22_uninf_up_sig' not foundpp(file="images/z22_uninf_up_gp_bp.png", image=z22_uninf_up_gp$pvalue_plots$bpp_plot_over, height=20, width=10)## Error in pp(file = "images/z22_uninf_up_gp_bp.png", image = z22_uninf_up_gp$pvalue_plots$bpp_plot_over, : object 'z22_uninf_up_gp' not foundz22_uninf_down_gp <- simple_gprofiler(z22_uninf_down_sig)## Error in simple_gprofiler(z22_uninf_down_sig): object 'z22_uninf_down_sig' not foundz22_sbuninf_up_gp <- simple_gprofiler(z22_sbuninf_up_sig)## Error in simple_gprofiler(z22_sbuninf_up_sig): object 'z22_sbuninf_up_sig' not foundz22_sbuninf_down_gp <- simple_gprofiler(z22_sbuninf_down_sig)## Error in simple_gprofiler(z22_sbuninf_down_sig): object 'z22_sbuninf_down_sig' not foundz23_uninf_up_gp <- simple_gprofiler(z23_uninf_up_sig)## Error in simple_gprofiler(z23_uninf_up_sig): object 'z23_uninf_up_sig' not foundpp(file="images/z23_uninf_up_gp_bp.png", image=z23_uninf_up_gp$pvalue_plots$bpp_plot_over, height=20, width=10)## Error in pp(file = "images/z23_uninf_up_gp_bp.png", image = z23_uninf_up_gp$pvalue_plots$bpp_plot_over, : object 'z23_uninf_up_gp' not foundsanitize_columns <- c("donor", "drug", "condition", "batch", "macrophagetreatment",
"macrophageinfectionzymodeme")
library(org.Lpanamensis.MHOMCOL81L13.v46.eg.db)## Loading required package: AnnotationDbi## pan_db <- org.Lpanamensis.MHOMCOL81L13.v46.eg.db
all_lp_annot <- sm(load_orgdb_annotations(
pan_db,
keytype = "gid",
fields = c("annot_gene_entrez_id", "annot_gene_name",
"annot_strand", "annot_chromosome", "annot_cds_length",
"annot_gene_product")))$genes
macr_lp <- create_expt(metadata="sample_sheets/tmrc2_macrophage_samples_202203.xlsx",
gene_info=all_lp_annot, file_column = "lpanamensisv36hisatfile")## Reading the sample metadata.## The sample definitions comprises: 28 rows(samples) and 67 columns(metadata fields).## Error in dirname(filenames): object 'filenames' not found exclude_genes_expt(column = "gene_biotype", method = "keep",
pattern = "protein_coding") %>%
subset_expt(subset="typeofcells=='Macrophages'") %>%
subset_expt(nonzero = 11000) %>%
set_expt_factors(columns = sanitize_columns) %>%
set_expt_factors(columns=sanitize_columns, class="factor") %>%
set_expt_batches(fact="macrophagetreatment") %>%
set_expt_conditions(fact="macrophageinfectionzymodeme")## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': error in evaluating the argument 'object' in selecting a method for function 'pData': error in evaluating the argument 'object' in selecting a method for function 'fData': error in evaluating the argument 'object' in selecting a method for function 'fData': error in evaluating the argument 'object' in selecting a method for function 'sampleNames': error in evaluating the argument 'object' in selecting a method for function 'sampleNames': argument "expt" is missing, with no defaultif (!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))
}## If you wish to reproduce this exact build of hpgltools, invoke the following:## > git clone http://github.com/abelew/hpgltools.git## > git reset c07ff314c871617d0f3c45257d3c46e61270ed3e## This is hpgltools commit: Thu Mar 17 11:25:56 2022 -0400: c07ff314c871617d0f3c45257d3c46e61270ed3e## Saving to tmrc2_macrophage_202203.rda.xztmp <- loadme(filename=savefile)