Skip to content

GitLab

Commit 9ee74d5b authored by Lena Hersemann's avatar Lena Hersemann
Browse files

fixed bug concerning biomart database selection

parent f74a8f8c
Hide whitespace changes
Inline Side-by-side
common/cp_enrichment.R
View file @ 9ee74d5b
...@@ -523,9 +523,9 @@ stopifnot(map_lgl(pathwayPlots, ~ file.exists(.$plotfile)) %>% all) ...@@ -523,9 +523,9 @@ stopifnot(map_lgl(pathwayPlots, ~ file.exists(.$plotfile)) %>% all)
install_package("biomaRt") install_package("biomaRt")
library(rapportools)
## prepare tooltips with expression scores ## prepare tooltips with expression scores
biomart_db <- ifelse(!is.null(opts$biomart_database), opts$biomart_database, guess_mart(geneLists$ensembl_gene_id)) biomart_db <- ifelse(!is.empty(opts$biomart_database), opts$biomart_database, guess_mart(geneLists$ensembl_gene_id))
ens2entrez <- quote({ ens2entrez <- quote({
# mart <- biomaRt::useDataset(guess_mart(geneLists$ensembl_gene_id), mart = biomaRt::useMart("ensembl")) # mart <- biomaRt::useDataset(guess_mart(geneLists$ensembl_gene_id), mart = biomaRt::useMart("ensembl"))
## todo fix this https://support.bioconductor.org/p/74322/ ## todo fix this https://support.bioconductor.org/p/74322/
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment