Hi All, I am analyzing a chip seq data trying to identify DNA binding sites to a specific protein.I did the alignment using bwa, and peaks calling using macs2. Now I am using R package "chipseeker" to annotate these peaks. My question is how can I excluded micro-RNA encoding genes from the annotation. I would guess that I have to remove them from the txdb I used for annotating the peaks. Is there an easy way to do this?
library(ChIPseeker) library("TxDb.Hsapiens.UCSC.hg38.knownGene") txdb<-TxDb.Hsapiens.UCSC.hg38.knownGene peakAnnotation <- annotatePeak("narrowpeak_bowtie_q0.05_IgG.txt", tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Hs.eg.db")