Question: Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
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gravatar for sutturka
7 weeks ago by
sutturka0
sutturka0 wrote:

Recently I noticed that using the org.Hs.eg.db database annotated specific genes (e.g. CASC15, ACTR3BP5, STAG3L3) with ENSEMBL IDs as "NA". This could be the limitation of database.

I tried EnsDb.Hsapiens.v86 which could determine the correct ENSEMBL IDs for these features.

library(EnsDb.Hsapiens.v86)

edb <- EnsDb.Hsapiens.v86
transcripts(edb, filter = GeneNameFilter("CASC15"))

I was able to use the same database in ChIPSeeker without any issues but somehow it does not captured the ENSEMBL ID which is available in the column named gene_id.

library(ChIPseeker)

Anno <- annotatePeak(bedfile, tssRegion=c(-3000, 3000), TxDb=TxDb.Hsapiens.UCSC.hg38.knownGene, annoDb=EnsDb.Hsapiens.v86)

This fetched the annotation columns "geneId", "transcriptId", "distanceToTSS", "SYMBOL", "GENENAME". How to modify the ChIPSeeker code to get the column "gene_id" from the EnsDb.Hsapiens.v86 database?

Thanks

chipseeker • 101 views
ADD COMMENTlink written 7 weeks ago by sutturka0

annotatePeak is hard-coded to look for geneId, not gene_id - see here: https://github.com/YuLab-SMU/ChIPseeker/blob/master/R/annotatePeak.R#L178

You may want to create an issue on the GitHub page, and/or literally edit the column name of the object EnsDb.Hsapiens.v86

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by Kevin Blighe340
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