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Commit aea6b362 authored by Holger Brandl's avatar Holger Brandl
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deseq workflow cosmetics

parent 5b9dc042
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......@@ -39,7 +39,7 @@ count_matrix_file <- opts$count_matrix
design_matrix_file <- opts$design_matrix
contrasts_file <- opts$contrasts
resultsBase <- if(str_length(opts$out)>0) paste0(opts$outprefix, ".") else ""
resultsBase <- if(str_length(opts$out)>0) paste0(opts$out, ".") else ""
pcutoff <- if(is.null(opts$pcutoff)) NULL else as.numeric(opts$pcutoff)
qcutoff <- if(is.numeric(pcutoff)) NULL else as.numeric(opts$qcutoff)
......@@ -49,7 +49,7 @@ if(is.numeric(pcutoff)) opts$qcutoff <- NULL
designFormula <- opts$design
## consider last element of design formula as sample attribute
contrastAttribute <- str_split(designFormula, "[+]") %>% unlist() %>% tail(1)
assert(designFormula!="sample" && !is.null(design_matrix_file), "custom designs are not supported without a design matrix")
assert(designFormula=="sample" || !is.null(design_matrix_file), "custom designs are not supported without a design matrix")
#' # Differential Expression Analysis
......@@ -434,7 +434,7 @@ geneInfo <- quote({
}) %>% cache_it("geneInfo")
## save as reference for downstream analysis
write_tsv(geneInfo, path="geneInfo.txt")
write_tsv(geneInfo, path=paste0(resultsBase, "geneInfo.txt"))
#' Export counts per replicate as double-normalized FPKMs=(read_count * 10^9)/(gene_length * library_size)
......@@ -450,10 +450,11 @@ fpkms <- countMatrix %>%
#fpkms %>% ggplot(aes(fpkm)) + geom_histogram() + scale_x_log10(labels=comma)
write_tsv(fpkms, "fpkms_by_replicate.long.txt")
write_tsv(fpkms, paste0(resultsBase, "fpkms_by_replicate.long.txt"))
fpkms %>%
transmute(ensembl_gene_id, replicate, fpkm) %>%
spread(replicate, fpkm) %>% write_tsv("fpkms_by_replicate.wide.txt")
spread(replicate, fpkm) %>%
write_tsv(paste0(resultsBase, "fpkms_by_replicate.wide.txt"))
#' Also export averaged counts per sample as double-normalized FPKMs=(read_count * 10^9)/(gene_length * library_size)
......@@ -477,10 +478,10 @@ sampleFpkms <- countMatrix %>%
#fpkms %>% ggplot(aes(fpkm)) + geom_histogram() + scale_x_log10(labels=comma)
write_tsv(sampleFpkms, "fpkms_by_sample.long.txt")
write_tsv(sampleFpkms, paste0(resultsBase, "fpkms_by_sample.long.txt"))
sampleFpkms %>%
transmute(ensembl_gene_id, sample, fpkm) %>%
spread(sample, fpkm) %>% write_tsv("fpkms_by_sample.wide.txt")
spread(sample, fpkm) %>% write_tsv(paste0(resultsBase, "fpkms_by_sample.wide.txt"))
#' [FPKMs as table](fpkms.long.txt) [FPKMs as Matrix](fpkms.wide.txt)
......
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