Commit f71f7453 authored by Lena Hersemann's avatar Lena Hersemann

added test to make sure that sample names of the count matrix and the design...

added test to make sure that sample names of the count matrix and the design matrix match; cosmetics
parent b54d9486
......@@ -49,7 +49,7 @@ load_pack(edgeR)
#-----------------------------------------------------------------------------------------------------------------------
results_prefix = "limma_diffex"
results_prefix = "limma"
## process input arguments
......@@ -98,6 +98,9 @@ kable(expDesign)
#' count matrix:
countData = read_tsv(count_matrix_file) %T>% glimpse
if(!str_detect(expDesign$replicate, paste0(colnames(countData), sep = "|"))) { stop("ATTENTION: sample names of the count matrix and exp_design do not match") }
# import protein information
if (is.null(protein_info_file)) {
protein_info = distinct(countData, protein_ids)
......@@ -596,11 +599,9 @@ left_join(voom_before %>% rename(x_voom = x, y_voom = y),
#' | File | Description |
#' |------|------|
#' | [diffex_genes.txt](diffex_genes.txt) | list of all differentially expressed genes from the DESeq analysis - That's the file you are most likely looking for! |
#' | [de_results.txt](de_results.txt) | list of all genes from the DESeq analysis |
#' | [norm_exp_by_condition.txt](norm_exp_by_condition.txt) | tpm values of the different conditions |
#' | [norm_exp_by_replicate.txt](norm_exp_by_replicate.txt) | tpm values of individual replicates |
#' | [geneInfo.txt](geneInfo.txt) | general gene information |
#' | [limma.diff_proteins.txt](limma.diff_proteins.txt) | list of all differentially abundant protein groups from the limma analysis - That's the file you are most likely looking for! |
#' | [limma.da_results.txt](limma.da_results.txt) | list of all protein groups from the limma analysis |
#' | [limma.geneInfo.txt](limma.geneInfo.txt) | general gene information |
#'
#-----------------------------------------------------------------------------------------------------------------------
......
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