What is the codification in genestrand 1 and 2?
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2.6 years ago
Lila M ★ 1.2k

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!

chipseeker peakannotation • 603 views
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