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.
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
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