Commit a88ffae4 authored by Holger Brandl's avatar Holger Brandl

more consistent argument naming

parent dbcf747a
......@@ -17,7 +17,7 @@ Options:
--design <formula> Design fomula for DeSeq with contrast attribute at the end [default: condition]
--lfc <lfc_cutoff> Just report genes with abs(lfc) > lfc_cutoff as hits [default: 1.0]
--ensembl_db <ensembl_db> Ensebmbl db to be used. If not specified inferred from data. TODO implement NONE here!!
--geneInfo <info_file> Gene information file downloaded from the ensembl website if bioMart version is not present
--gene_info <info_file> Gene information file downloaded from the ensembl website if bioMart version is not present
--betaprior <boolean> Apply betaprior when running DESeq2 [default: TRUE]
'
......@@ -48,7 +48,8 @@ count_matrix_file = opts$count_matrix
design_matrix_file = opts$design_matrix
contrasts_file = opts$contrasts
use_betaPrior = as.logical(opts$betaprior)
gene_info_file = opts$geneInfo
gene_info_file = opts$gene_info
assert(is.null(gene_info_file) || file.exists(gene_info_file), "invalid gene_info_file")
resultsBase = if (str_length(opts$out) > 0) paste0(opts$out, ".") else ""
......@@ -645,11 +646,12 @@ deResults %>%
install_package("biomaRt")
ensembl_dataset= if (!is.null(opts$ensembl_db)) paste0(opts$ensembl_db, "_gene_ensembl") else guess_mart(countData$ensembl_gene_id)
# Load transcriptome annotations needed for results annotation
if (is.null(gene_info_file)){
ensembl_dataset= if (!is.null(opts$ensembl_db)) paste0(opts$ensembl_db, "_gene_ensembl") else guess_mart(countData$ensembl_gene_id)
geneInfo = quote({
## mart = biomaRt::useDataset("drerio_gene_ensembl", mart = biomaRt::useMart("ensembl"))??
# mart = biomaRt::useDataset(guess_mart(countData$ensembl_gene_id), mart = biomaRt::useMart("ensembl"))
......
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