Commit 83be95a6 authored by Lena Hersemann's avatar Lena Hersemann

removed default settings for --project_prefix and --biomart_database

parent 32cc19ec
......@@ -11,9 +11,9 @@ Usage: cp_enrichment.R [options] <gene_lists_tsv> <group_col>
Options:
--overlay_expr_data Tsv with overlay data for the kegg pathways
--project <project_prefix> Name to prefix all generated result files [default: ]
--project <project_prefix> Name to prefix all generated result files
--qcutoff <qcutoff> Use a q-value cutoff of 0.01 instead of a q-value cutoff [default: 0.01]
--biomart_database Name of biomart database - if not provided it will be guessed by the ensembl gene ids [default: ]
--biomart_database Name of biomart database - if not provided it will be guessed by the ensembl gene ids
'
# commandArgs <- function(x) c("--overlay_expr_data", "../plot_score_matrix.txt", "../degs_by_contrast.txt", "contrast")
......@@ -67,7 +67,7 @@ if (! is.null(opts$overlay_expr_data)) {
## see http://www.bioconductor.org/packages/release/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.pdf for details
# resultsBaseName <- if (str_length(opts$project) > 0) paste0(opts$project, ".") else basename(opts$gene_lists_tsv) %>% trim_ext("txt") #%>% paste0(".")
resultsBaseName <- if (str_length(opts$project) > 0) paste0(opts$project, ".") else ""
resultsBaseName <- if (!is.null(opts$project)) paste0(opts$project, ".") else ""
#resultsBaseName=basename(opts$gene_lists_tsv) %>% trim_ext("txt") #%>% paste0(".")
q_cutoff <- as.numeric(opts$qcutoff)
......
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