Commit bcb9b774 authored by Lena Hersemann's avatar Lena Hersemann

added option to directly provide biomart database

parent 1a996c1c
......@@ -13,6 +13,7 @@ Options:
--overlay_expr_data Tsv with overlay data for the kegg pathways
--project <project_prefix> Name to prefix all generated result files [default: ]
--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: ]
'
# commandArgs <- function(x) c("--overlay_expr_data", "../plot_score_matrix.txt", "../degs_by_contrast.txt", "contrast")
......@@ -522,13 +523,16 @@ stopifnot(map_lgl(pathwayPlots, ~ file.exists(.$plotfile)) %>% all)
install_package("biomaRt")
## prepare tooltips with expression scores
biomart_db <- ifelse(!is.null(opts$biomart_database), opts$biomart_database, guess_mart(geneLists$ensembl_gene_id))
ens2entrez <- quote({
# mart <- biomaRt::useDataset(guess_mart(geneLists$ensembl_gene_id), mart = biomaRt::useMart("ensembl"))
## todo fix this https://support.bioconductor.org/p/74322/
# mart <- biomaRt::useDataset(guess_mart(geneLists$ensembl_gene_id), mart = biomaRt::useMart("ENSEMBL_MART_ENSEMBL", host = "www.ensembl.org"))
mart = biomaRt::useMart("ENSEMBL_MART_ENSEMBL",
dataset = guess_mart(geneLists$ensembl_gene_id),
# dataset = guess_mart(geneLists$ensembl_gene_id),
dataset = biomart_db,
host = "aug2017.archive.ensembl.org",
path = "/biomart/martservice",
archive = FALSE
......
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