Lets get a set of core shared genes among the three main species: L. major, L.mexicana, and L.panamensis. I am not sure how I want to deal with multi-copy genes yet.
meta <- EuPathDB::download_eupath_metadata(webservice="tritrypdb")
lm_entry <- EuPathDB::get_eupath_entry(species="Leishmania major", metadata=meta)## Found the following hits: Leishmania major Friedlin, Leishmania major LV39c5, Leishmania major SD75.1, choosing the first.## Using: Leishmania major Friedlin.lp_entry <- EuPathDB::get_eupath_entry(species="Leishmania panamensis", metadata=meta)## Found the following hits: Leishmania panamensis MHOMCOL81L13, Leishmania panamensis MHOMPA94PSC1, choosing the first.## Using: Leishmania panamensis MHOMCOL81L13.lmex_entry <- EuPathDB::get_eupath_entry(species="Leishmania mexicana", metadata=meta)## Found: Leishmania mexicana MHOMGT2001U1103lama_entry <- EuPathDB::get_eupath_entry(species="Leishmania amazonensis", metadata=meta)## Found: Leishmania amazonensis MHOMBR71973M2269lb_entry <- EuPathDB::get_eupath_entry(species="2904", metadata=meta)## Found the following hits: Leishmania braziliensis MHOMBR75M2904, Leishmania braziliensis MHOMBR75M2904_2019, choosing the first.## Using: Leishmania braziliensis MHOMBR75M2904.##lm_db <- EuPathDB::make_eupath_orgdb(entry=lm_entry, installp=TRUE, reinstall=TRUE, overwrite=TRUE)
lm_db <- EuPathDB::make_eupath_orgdb(entry=lm_entry)## Starting creation of org.Lmajor.Friedlin.v50.eg.db.## [WARN] API request failed for Leishmania major Friedlin (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania major Friedlin (code =
## 422):## [WARN] API request failed for Leishmania major Friedlin (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania major Friedlin (code =
## 422):## [WARN] API request failed for Leishmania major Friedlin (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania major Friedlin (code =
## 422):## [WARN] API request failed for Leishmania major Friedlin (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania major Friedlin (code =
## 422):## [WARN] API request failed for Leishmania major Friedlin (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania major Friedlin (code =
## 422):## [WARN] API request failed for Leishmania major Friedlin (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania major Friedlin (code =
## 422):## Setting NA to numeric.## Error in if (names(x)[nc] == "") names(x)[nc] <- paste0("V", nc) :
## missing value where TRUE/FALSE needed## Warning in EuPathDB::make_eupath_orgdb(entry = lm_entry): Unable to create an
## orgdb for this species.##lmex_db <- EuPathDB::make_eupath_orgdb(entry=lmex_entry, installp=TRUE, reinstall=TRUE, overwrite=TRUE)
lmex_db <- EuPathDB::make_eupath_orgdb(entry=lmex_entry)## Starting creation of org.Lmexicana.MHOMGT2001U1103.v50.eg.db.## [WARN] API request failed for Leishmania mexicana MHOMGT2001U1103 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania mexicana MHOMGT2001U1103
## (code = 422):## [WARN] API request failed for Leishmania mexicana MHOMGT2001U1103 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania mexicana MHOMGT2001U1103
## (code = 422):## [WARN] API request failed for Leishmania mexicana MHOMGT2001U1103 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania mexicana MHOMGT2001U1103
## (code = 422):## [WARN] API request failed for Leishmania mexicana MHOMGT2001U1103 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania mexicana MHOMGT2001U1103
## (code = 422):## [WARN] API request failed for Leishmania mexicana MHOMGT2001U1103 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania mexicana MHOMGT2001U1103
## (code = 422):## [WARN] API request failed for Leishmania mexicana MHOMGT2001U1103 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania mexicana MHOMGT2001U1103
## (code = 422):## Setting NA to numeric.## Error in if (names(x)[nc] == "") names(x)[nc] <- paste0("V", nc) :
## missing value where TRUE/FALSE needed## Warning in EuPathDB::make_eupath_orgdb(entry = lmex_entry): Unable to create an
## orgdb for this species.##lp_db <- EuPathDB::make_eupath_orgdb(entry=lp_entry, installp=TRUE, reinstall=TRUE, overwrite=TRUE)
lp_db <- EuPathDB::make_eupath_orgdb(entry=lp_entry)## Starting creation of org.Lpanamensis.MHOMCOL81L13.v50.eg.db.## [WARN] API request failed for Leishmania panamensis MHOMCOL81L13 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania panamensis MHOMCOL81L13
## (code = 422):## [WARN] API request failed for Leishmania panamensis MHOMCOL81L13 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania panamensis MHOMCOL81L13
## (code = 422):## [WARN] API request failed for Leishmania panamensis MHOMCOL81L13 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania panamensis MHOMCOL81L13
## (code = 422):## [WARN] API request failed for Leishmania panamensis MHOMCOL81L13 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania panamensis MHOMCOL81L13
## (code = 422):## [WARN] API request failed for Leishmania panamensis MHOMCOL81L13 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania panamensis MHOMCOL81L13
## (code = 422):## [WARN] API request failed for Leishmania panamensis MHOMCOL81L13 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania panamensis MHOMCOL81L13
## (code = 422):## Setting NA to numeric.## Error in if (names(x)[nc] == "") names(x)[nc] <- paste0("V", nc) :
## missing value where TRUE/FALSE needed## Warning in EuPathDB::make_eupath_orgdb(entry = lp_entry): Unable to create an
## orgdb for this species.##la_db <- EuPathDB::make_eupath_orgdb(entry=lama_entry, installp=TRUE, reinstall=TRUE, overwrite=TRUE)
la_db <- EuPathDB::make_eupath_orgdb(entry=lama_entry)## Starting creation of org.Lamazonensis.MHOMBR71973M2269.v50.eg.db.## [WARN] API request failed for Leishmania amazonensis MHOMBR71973M2269 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania amazonensis
## MHOMBR71973M2269 (code = 422):## [WARN] API request failed for Leishmania amazonensis MHOMBR71973M2269 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania amazonensis
## MHOMBR71973M2269 (code = 422):## [WARN] API request failed for Leishmania amazonensis MHOMBR71973M2269 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania amazonensis
## MHOMBR71973M2269 (code = 422):## [WARN] API request failed for Leishmania amazonensis MHOMBR71973M2269 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania amazonensis
## MHOMBR71973M2269 (code = 422):## [WARN] API request failed for Leishmania amazonensis MHOMBR71973M2269 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania amazonensis
## MHOMBR71973M2269 (code = 422):## [WARN] API request failed for Leishmania amazonensis MHOMBR71973M2269 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania amazonensis
## MHOMBR71973M2269 (code = 422):## Setting NA to numeric.## Error in if (names(x)[nc] == "") names(x)[nc] <- paste0("V", nc) :
## missing value where TRUE/FALSE needed## Warning in EuPathDB::make_eupath_orgdb(entry = lama_entry): Unable to create an
## orgdb for this species.##lb_db <- EuPathDB::make_eupath_orgdb(entry=lb_entry, installp=TRUE, reinstall=TRUE, overwrite=TRUE)
lb_db <- EuPathDB::make_eupath_orgdb(entry=lb_entry)## Starting creation of org.Lbraziliensis.MHOMBR75M2904.v50.eg.db.## [WARN] API request failed for Leishmania braziliensis MHOMBR75M2904 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania braziliensis MHOMBR75M2904
## (code = 422):## [WARN] API request failed for Leishmania braziliensis MHOMBR75M2904 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania braziliensis MHOMBR75M2904
## (code = 422):## [WARN] API request failed for Leishmania braziliensis MHOMBR75M2904 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania braziliensis MHOMBR75M2904
## (code = 422):## [WARN] API request failed for Leishmania braziliensis MHOMBR75M2904 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania braziliensis MHOMBR75M2904
## (code = 422):## [WARN] API request failed for Leishmania braziliensis MHOMBR75M2904 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania braziliensis MHOMBR75M2904
## (code = 422):## [WARN] API request failed for Leishmania braziliensis MHOMBR75M2904 (code = 422):## Warning in warn(sprintf("API request failed for %s (code = 422): ",
## entry[["Taxon"]])): API request failed for Leishmania braziliensis MHOMBR75M2904
## (code = 422):## Setting NA to numeric.## Error in if (names(x)[nc] == "") names(x)[nc] <- paste0("V", nc) :
## missing value where TRUE/FALSE needed## Warning in EuPathDB::make_eupath_orgdb(entry = lb_entry): Unable to create an
## orgdb for this species.lm_annot <- EuPathDB::load_eupath_annotations(entry=lm_entry)## Error in EuPathDB::load_eupath_annotations(entry = lm_entry): unused argument (entry = lm_entry)lmex_annot <- EuPathDB::load_eupath_annotations(entry=lmex_entry)## Error in EuPathDB::load_eupath_annotations(entry = lmex_entry): unused argument (entry = lmex_entry)lpan_annot <- EuPathDB::load_eupath_annotations(entry=lp_entry)## Error in EuPathDB::load_eupath_annotations(entry = lp_entry): unused argument (entry = lp_entry)lama_annot <- EuPathDB::load_eupath_annotations(entry=lama_entry)## Error in EuPathDB::load_eupath_annotations(entry = lama_entry): unused argument (entry = lama_entry)lbraz_annot <- EuPathDB::load_eupath_annotations(entry=lb_entry)## Error in EuPathDB::load_eupath_annotations(entry = lb_entry): unused argument (entry = lb_entry)lm_ortho <- EuPathDB::extract_eupath_orthologs(lm_db)## Error in EuPathDB::extract_eupath_orthologs(lm_db): I only understand orgdbs or the name of a species.lmex_ortho <- EuPathDB::extract_eupath_orthologs(lmex_db)## Error in EuPathDB::extract_eupath_orthologs(lmex_db): I only understand orgdbs or the name of a species.lp_ortho <- EuPathDB::extract_eupath_orthologs(lp_db)## Error in EuPathDB::extract_eupath_orthologs(lp_db): I only understand orgdbs or the name of a species.la_ortho <- EuPathDB::extract_eupath_orthologs(la_db)## Error in EuPathDB::extract_eupath_orthologs(la_db): I only understand orgdbs or the name of a species.lb_ortho <- EuPathDB::extract_eupath_orthologs(lb_db)## Error in EuPathDB::extract_eupath_orthologs(lb_db): I only understand orgdbs or the name of a species.sample_sheet <- "sample_sheets/UMD_leishmania_host_metasheet_20200227.xlsx"
lm_expt_annot <- lm_annot## Error in eval(expr, envir, enclos): object 'lm_annot' not foundrownames(lm_expt_annot) <- paste0(rownames(lm_expt_annot), ".mRNA")## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'lm_expt_annot' not foundlm_expt <- create_expt(metadata=sample_sheet,
gene_info=lm_expt_annot,
savefile="lmajor.rda",
file_column="lmajorfile")## Reading the sample metadata.## Dropped 2 rows from the sample metadata because they were blank.## The sample definitions comprises: 441 rows(samples) and 67 columns(metadata fields).## Reading count tables.## Reading salmon data with tximport.## Finished reading count data.## Warning in create_expt(metadata = sample_sheet, gene_info = lm_expt_annot, :
## Some samples were removed when cross referencing the samples against the count
## data.## Error in create_expt(metadata = sample_sheet, gene_info = lm_expt_annot, : object 'lm_expt_annot' not foundlmex_expt_annot <- lmex_annot## Error in eval(expr, envir, enclos): object 'lmex_annot' not foundrownames(lmex_expt_annot) <- paste0(rownames(lmex_expt_annot), ".1")## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'lmex_expt_annot' not foundlmex_expt <- create_expt(metadata=sample_sheet,
gene_info=lmex_expt_annot,
savefile="lmexicana.rda",
file_column="lmexicanafile")## Reading the sample metadata.## Dropped 2 rows from the sample metadata because they were blank.## The sample definitions comprises: 441 rows(samples) and 67 columns(metadata fields).## Reading count tables.## Reading salmon data with tximport.## Finished reading count data.## Warning in create_expt(metadata = sample_sheet, gene_info = lmex_expt_annot, :
## Some samples were removed when cross referencing the samples against the count
## data.## Error in create_expt(metadata = sample_sheet, gene_info = lmex_expt_annot, : object 'lmex_expt_annot' not foundlp_expt_annot <- lpan_annot## Error in eval(expr, envir, enclos): object 'lpan_annot' not foundrownames(lp_expt_annot) <- paste0(rownames(lp_expt_annot), ".1")## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'lp_expt_annot' not foundlp_expt <- create_expt(metadata=sample_sheet,
gene_info=lp_expt_annot,
savefile="lpanamensis.rda",
file_column="lpanamensisfile")## Reading the sample metadata.## Dropped 2 rows from the sample metadata because they were blank.## The sample definitions comprises: 441 rows(samples) and 67 columns(metadata fields).## Reading count tables.## Reading salmon data with tximport.## Finished reading count data.## Warning in create_expt(metadata = sample_sheet, gene_info = lp_expt_annot, :
## Some samples were removed when cross referencing the samples against the count
## data.## Error in create_expt(metadata = sample_sheet, gene_info = lp_expt_annot, : object 'lp_expt_annot' not foundla_expt_annot <- lama_annot## Error in eval(expr, envir, enclos): object 'lama_annot' not foundrownames(la_expt_annot) <- paste0(rownames(la_expt_annot), ".1")## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'la_expt_annot' not foundla_expt <- create_expt(metadata=sample_sheet,
gene_info=la_expt_annot,
savefile="lamazonensis.rda",
file_column="lamazonensisfile")## Reading the sample metadata.## Dropped 2 rows from the sample metadata because they were blank.## The sample definitions comprises: 441 rows(samples) and 67 columns(metadata fields).## Reading count tables.## Reading salmon data with tximport.## Finished reading count data.## Warning in create_expt(metadata = sample_sheet, gene_info = la_expt_annot, :
## Some samples were removed when cross referencing the samples against the count
## data.## Error in create_expt(metadata = sample_sheet, gene_info = la_expt_annot, : object 'la_expt_annot' not foundlb_expt_annot <- lbraz_annot## Error in eval(expr, envir, enclos): object 'lbraz_annot' not foundrownames(lb_expt_annot) <- paste0(rownames(lb_expt_annot), ".mRNA")## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'lb_expt_annot' not foundlb_expt <- create_expt(metadata=sample_sheet,
gene_info=lb_expt_annot,
savefile="lbraziliensis.rda",
file_column="lbraziliensisfile")## Reading the sample metadata.## Dropped 2 rows from the sample metadata because they were blank.## The sample definitions comprises: 441 rows(samples) and 67 columns(metadata fields).## Reading count tables.## Reading salmon data with tximport.## Finished reading count data.## Warning in create_expt(metadata = sample_sheet, gene_info = lb_expt_annot, :
## Some samples were removed when cross referencing the samples against the count
## data.## Error in create_expt(metadata = sample_sheet, gene_info = lb_expt_annot, : object 'lb_expt_annot' not foundsub_cols <- c("GID", "ORTHOLOGS_ID", "ORTHOLOGS_GROUP")
lmlp_idx <- lm_ortho[["ORTHOLOGS_SPECIES"]] == "Leishmania panamensis MHOM/COL/81/L13"## Error in eval(expr, envir, enclos): object 'lm_ortho' not foundlplm_idx <- lp_ortho[["ORTHOLOGS_SPECIES"]] == "Leishmania major strain Friedlin"## Error in eval(expr, envir, enclos): object 'lp_ortho' not foundlmlp_ortho <- lm_ortho[lmlp_idx, sub_cols]## Error in eval(expr, envir, enclos): object 'lm_ortho' not foundlplm_ortho <- lp_ortho[lplm_idx, sub_cols]## Error in eval(expr, envir, enclos): object 'lp_ortho' not foundlm_mtrx <- exprs(lm_expt)## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'exprs': object 'lm_expt' not foundrownames(lm_mtrx) <- gsub(pattern="\\.mRNA", replacement="", x=rownames(lm_mtrx))## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'lm_mtrx' not foundlm_des <- pData(lm_expt)## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': object 'lm_expt' not foundlm_annot <- fData(lm_expt)## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'fData': object 'lm_expt' not foundlp_mtrx <- exprs(lp_expt)## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'exprs': object 'lp_expt' not foundrownames(lp_mtrx) <- gsub(pattern="\\.1", replacement="", x=rownames(lp_mtrx))## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'rownames': object 'lp_mtrx' not foundlp_des <- pData(lp_expt)## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'pData': object 'lp_expt' not foundlp_annot <- fData(lp_expt)## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'fData': object 'lp_expt' not foundcolnames(lmlp_ortho) <- c("lm_gid", "lp_gid", "ogid")## Error in colnames(lmlp_ortho) <- c("lm_gid", "lp_gid", "ogid"): object 'lmlp_ortho' not foundcolnames(lplm_ortho) <- c("lp_gid", "lm_gid", "ogid")## Error in colnames(lplm_ortho) <- c("lp_gid", "lm_gid", "ogid"): object 'lplm_ortho' not foundcombined_ids <- merge(lmlp_ortho, lplm_ortho, all=TRUE)## Error in merge(lmlp_ortho, lplm_ortho, all = TRUE): object 'lmlp_ortho' not foundogids <- unique(combined_ids[["ogid"]])## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'unique': object 'combined_ids' not foundexprs <- data.frame(row.names=ogids)## Error in data.frame(row.names = ogids): object 'ogids' not foundfor (m in 1:ncol(lm_mtrx)) {
name <- colnames(lm_mtrx)[m]
exprs[[name]] <- 0
}## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'ncol': object 'lm_mtrx' not foundfor (p in 1:ncol(lp_mtrx)) {
name <- colnames(lp_mtrx)[p]
exprs[[name]] <- 0
}## Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'ncol': object 'lp_mtrx' not foundfor (i in 1:length(ogids)) {
ogid <- ogids[i]
og_idx <- combined_ids[["ogid"]] == ogid
lm_ids <- unique(combined_ids[og_idx, "lm_gid"])
lp_ids <- unique(combined_ids[og_idx, "lp_gid"])
lm_idx <- rownames(lm_mtrx) == lm_ids
lp_idx <- rownames(lp_mtrx) == lp_ids
if (sum(lm_idx) == 1) {
lm_sum <- lm_mtrx[lm_idx, ]
} else {
lm_sum <- colSums(lm_mtrx[lm_idx, ])
}
if (sum(lp_idx) == 1) {
lp_sum <- lp_mtrx[lp_idx, ]
} else {
lp_sum <- colSums(lp_mtrx[lp_idx, ])
}
sum <- c(lm_sum, lp_sum)
exprs[ogid, ] <- sum
}## Error in eval(expr, envir, enclos): object 'ogids' not foundpander::pander(sessionInfo())R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
locale: LC_CTYPE=en_US.UTF-8, LC_NUMERIC=C, LC_TIME=en_US.UTF-8, LC_COLLATE=en_US.UTF-8, LC_MONETARY=en_US.UTF-8, LC_MESSAGES=en_US.UTF-8, LC_PAPER=en_US.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_US.UTF-8 and LC_IDENTIFICATION=C
attached base packages: parallel, stats, graphics, grDevices, utils, datasets, methods and base
other attached packages: futile.logger(v.1.4.3), hpgltools(v.1.0), testthat(v.3.0.1), R6(v.2.5.0), Biobase(v.2.50.0) and BiocGenerics(v.0.36.0)
loaded via a namespace (and not attached): RUnit(v.0.4.32), tidyselect(v.1.1.0), lme4(v.1.1-26), RSQLite(v.2.2.2), AnnotationDbi(v.1.52.0), grid(v.4.0.3), BiocParallel(v.1.24.1), devtools(v.2.3.2), scatterpie(v.0.1.5), munsell(v.0.5.0), codetools(v.0.2-18), statmod(v.1.4.35), withr(v.2.4.0), colorspace(v.2.0-0), GOSemSim(v.2.16.1), OrganismDbi(v.1.32.0), knitr(v.1.30), rstudioapi(v.0.13), stats4(v.4.0.3), DOSE(v.3.16.0), MatrixGenerics(v.1.2.0), tximport(v.1.18.0), GenomeInfoDbData(v.1.2.4), polyclip(v.1.10-0), bit64(v.4.0.5), farver(v.2.0.3), rprojroot(v.2.0.2), downloader(v.0.4), vctrs(v.0.3.6), generics(v.0.1.0), lambda.r(v.1.2.4), xfun(v.0.19), BiocFileCache(v.1.14.0), doParallel(v.1.0.16), GenomeInfoDb(v.1.26.2), graphlayouts(v.0.7.1), locfit(v.1.5-9.4), bitops(v.1.0-6), fgsea(v.1.16.0), DelayedArray(v.0.16.0), assertthat(v.0.2.1), promises(v.1.1.1), scales(v.1.1.1), ggraph(v.2.0.4), enrichplot(v.1.10.1), gtable(v.0.3.0), biocViews(v.1.58.1), sva(v.3.38.0), processx(v.3.4.5), tidygraph(v.1.2.0), rlang(v.0.4.10), genefilter(v.1.72.0), splines(v.4.0.3), rtracklayer(v.1.50.0), broom(v.0.7.3), BiocManager(v.1.30.10), yaml(v.2.2.1), reshape2(v.1.4.4), GenomicFeatures(v.1.42.1), backports(v.1.2.1), httpuv(v.1.5.5), qvalue(v.2.22.0), RBGL(v.1.66.0), clusterProfiler(v.3.18.0), tools(v.4.0.3), usethis(v.1.6.3), ggplot2(v.3.3.3), ellipsis(v.0.3.1), gplots(v.3.1.1), RColorBrewer(v.1.1-2), sessioninfo(v.1.1.1), Rcpp(v.1.0.6), plyr(v.1.8.6), progress(v.1.2.2), zlibbioc(v.1.36.0), purrr(v.0.3.4), RCurl(v.1.98-1.2), ps(v.1.5.0), prettyunits(v.1.1.1), openssl(v.1.4.3), viridis(v.0.5.1), cowplot(v.1.1.0), S4Vectors(v.0.28.1), SummarizedExperiment(v.1.20.0), ggrepel(v.0.9.0), colorRamps(v.2.3), fs(v.1.5.0), variancePartition(v.1.20.0), magrittr(v.2.0.1), futile.options(v.1.0.1), data.table(v.1.13.6), openxlsx(v.4.2.3), DO.db(v.2.9), matrixStats(v.0.57.0), pkgload(v.1.1.0), mime(v.0.9), hms(v.1.0.0), evaluate(v.0.14), xtable(v.1.8-4), pbkrtest(v.0.5-0.1), XML(v.3.99-0.5), IRanges(v.2.24.1), gridExtra(v.2.3), compiler(v.4.0.3), biomaRt(v.2.46.0), tibble(v.3.0.5), KernSmooth(v.2.23-18), crayon(v.1.3.4), shadowtext(v.0.0.7), minqa(v.1.2.4), htmltools(v.0.5.1), later(v.1.1.0.1), mgcv(v.1.8-33), tidyr(v.1.1.2), DBI(v.1.1.1), formatR(v.1.7), tweenr(v.1.0.1), dbplyr(v.2.0.0), MASS(v.7.3-53), rappdirs(v.0.3.1), boot(v.1.3-25), readr(v.1.4.0), Matrix(v.1.3-0), cli(v.2.2.0), igraph(v.1.2.6), GenomicRanges(v.1.42.0), pkgconfig(v.2.0.3), rvcheck(v.0.1.8), GenomicAlignments(v.1.26.0), xml2(v.1.3.2), foreach(v.1.5.1), annotate(v.1.68.0), XVector(v.0.30.0), AnnotationForge(v.1.32.0), rvest(v.0.3.6), stringr(v.1.4.0), callr(v.3.5.1), digest(v.0.6.27), graph(v.1.68.0), Biostrings(v.2.58.0), EuPathDB(v.1.6.0), rmarkdown(v.2.6), fastmatch(v.1.1-0), edgeR(v.3.32.0), PROPER(v.1.22.0), curl(v.4.3), shiny(v.1.5.0), Rsamtools(v.2.6.0), gtools(v.3.8.2), nloptr(v.1.2.2.2), lifecycle(v.0.2.0), nlme(v.3.1-151), jsonlite(v.1.7.2), desc(v.1.2.0), viridisLite(v.0.3.0), askpass(v.1.1), limma(v.3.46.0), fansi(v.0.4.2), pillar(v.1.4.7), lattice(v.0.20-41), fastmap(v.1.0.1), httr(v.1.4.2), pkgbuild(v.1.2.0), survival(v.3.2-7), GO.db(v.3.12.1), interactiveDisplayBase(v.1.28.0), glue(v.1.4.2), remotes(v.2.2.0), zip(v.2.1.1), iterators(v.1.0.13), pander(v.0.6.3), BiocVersion(v.3.12.0), bit(v.4.0.4), ggforce(v.0.3.2), stringi(v.1.5.3), blob(v.1.2.1), AnnotationHub(v.2.22.0), caTools(v.1.18.0), AnnotationHubData(v.1.20.0), memoise(v.1.1.0), rBiopaxParser(v.2.30.0) and dplyr(v.1.0.3)
message(paste0("This is hpgltools commit: ", get_git_commit()))## If you wish to reproduce this exact build of hpgltools, invoke the following:## > git clone http://github.com/abelew/hpgltools.git## > git reset 052640a0b091e9a740e487957e087f265d0c74b5## This is hpgltools commit: Thu Dec 3 13:42:02 2020 -0500: 052640a0b091e9a740e487957e087f265d0c74b5## message(paste0("Saving to ", savefile))
## tmp <- sm(saveme(filename=savefile))