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Hello,
I've been trying to use biomaRt to get reactome IDs (from pathways) of given reactome_gene IDs, however I found out that the reactome_gene IDs ARE the pathway IDs. It is now not possible to get the matching pathways by these gene IDs.
For example
library(biomaRt) ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") reactomeID <- c("R-HSA-49155", "R-HSA-199420") getBM(attributes=c('reactome_gene', 'reactome'), filters = 'reactome_gene', values = reactomeID, mart = ensembl) [1] reactome_gene reactome <0 rows> (or 0-length row.names) getBM(attributes=c('reactome_gene', 'entrezgene'), filters = 'reactome_gene', values = 'R-HSA-49155', mart = ensembl) [1] reactome_gene reactome <0 rows> (or 0-length row.names)
However, when I use a pathway (reactome) ID instead of reactome_gene ID it does work, but this is not what I am asking to find.
getBM(attributes=c('reactome_gene', 'entrezgene'), filters = 'reactome_gene', values = 'R-HSA-110331', mart = ensembl) reactome_gene entrezgene 1 R-HSA-110331 4968 2 R-HSA-110331 4595 3 R-HSA-110331 4350
Is this a bug? Or am I missing something?