Entering edit mode
3.2 years ago
Lila M
★
1.3k
Hi there,
I'm doing some peak annotation using ChIPseeker
library(ChIPseeker)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(clusterProfiler)
library(annotables)
library(org.Hs.eg.db)
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
peaks= readPeakFile("peaks_", header = F)
peakAnno <- annotatePeak(peaks, tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Hs.eg.db")
peaks_annot <- as.data.frame(peakAnno)
In my annotation file "geneStrand"
is codified as 1 and 2 for the first time. I want to recode in + or -, but I'm not sure if 1 ==+ and 2 ==- (as below)
peaks_annot <- peaks_annot %>%
mutate(geneStrand=recode(geneStrand,
`+`=1,
`-`=2))
write.table(peaks_annot , file="results _annotation.txt", sep="\t", quote=F, row.names=F)
Do you guys know if I am right? Thank you!