I'm using the SBGNview package in R to visualize Reactome pathways, and am having problem with converting my gene IDs to pathwayCommons IDs.
Below is what I'm doing:
library(SBGNview)
library(org.Mmu.eg.db)
data("sbgn.xmls")
A <- matrix(c(1:20), nrow = 10, ncol = 2, byrow = TRUE)
colnames(A) <- c("exp1", "exp2")
rownames(A) <- c(57279, 18673, 11747, 240028, 13200, 67041, 67025, 73130, 54127, 14387)
changeDataId(data.input.id = A, input.type = "entrez", output.type = "pathwayCommons",
mol.type = "gene", org = "mmu")
This gives me the error:
Error in mol.sum.multiple.mapping(mol.data = data.input.id, id.map = id.map, :
no ID can be mapped!
However, I'm confused because I can find my entrez IDs in the mmu_pathwayCommons_ENTREZID database. For example, if I run the code below, I can find my ID in the database that I believe the changeDataID function uses.
>which(mmu_pathwayCommons_ENTREZID[,2] == "14387")
609645 609647 609649
609645 609647 609649
So why am I having trouble with converting the IDs?
•
written
by
garfield320 •
1 answer
As per the documentation for output.type, pathwayCommons is not supported but e.g. ensembl is, and changeDataId(data.input.id = A, input.type = "entrez", output.type = "ensembl", mol.type = "gene", org = "mmu") worked for me. Incidentally, this automatically loaded package org.Mm.eg.db.
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