Entering edit mode
Below is my code
library(ChIPseeker)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
files <- getSampleFiles()
options(ChIPseeker.downstreamDistance = 1000)
peakAnno <- annotatePeak(files[[4]], tssRegion=c(-3000, 3000),
TxDb=txdb)
plotAnnoPie(peakAnno)
options(ChIPseeker.downstreamDistance = 10)
peakAnno <- annotatePeak(files[[4]], tssRegion=c(-3000, 3000),
TxDb=txdb)
plotAnnoPie(peakAnno)
I find that no matter what number I enter in options(ChIPseeker.downstreamDistance = )
. The percent of downstream is same, But the number in plot indeed change.
The plot can be seen in https://github.com/YuLab-SMU/ChIPseeker/issues/112