annotatePeak error for some problem
Entering edit mode
Jones • 0
Last seen 18 days ago

hello, everyone: when I use ChIPseeker to annotatePeak my chip-seq peaks, some error came. When I use this function, I encounter some issues and would like to seek advice. How can I resolve this problem? I would greatly appreciate your help. my code is showing here:

annot <- annotatePeakInBatch(M_K9me2_1, TxDb = txdb,tssRegion = c(-3000, 3000),annoDb="org.At.tair.db")`
and the warning massage is "In annotatePeak(M_K9me2_1, TxDb = txdb, tssRegion = c(-3000, 3000),  :
  Unknown ID type, gene annotation will not be added...
ChIPseeker • 106 views
Entering edit mode
Last seen 1 day ago
United States

You don't say where you got the TxDb object, but it's probably going to fail regardless. The ID is identified by first looking at the metadata for the TxDb object, and then at the peaks GRanges object. And when looking at the GRanges object, it's only looking for Ensembl or NCBI gene IDs, so it's going to fail almost surely.

But that doesn't really matter. It's simple to annotate yourself. Just do something like

for(i in cn) mcols(annot)[[cn]] <- mapIds(org.At.tair.db, annot$geneID, cn, "TAIR")

You might need to inspect your annot object first to see where the TAIR symbols are (they are things like AT12121).

Login before adding your answer.

Traffic: 620 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6