Chapter 3 DiffBD-GenomeAnnotation

3.1 Description

Using ChIPseeker to annotate the lineage-conserved/specific CBSs based on genomic regions

3.2 Load data

file.ls <- list.files('data/DiffBD/', full.names = T, pattern = "bed")
peaks <- list(
  stable = file.ls[5],
  liver = file.ls[2],
  muscle = file.ls[3],
  bcell = file.ls[1])

3.3 Annotate

txdb = TxDb.Hsapiens.UCSC.hg19.knownGene
promoter <- getPromoters(TxDb = txdb, upstream = 2000, downstream = 2000)
peakAnnoList <- lapply(peaks, annotatePeak, TxDb=txdb,
                       tssRegion=c(-3000, 3000), verbose=FALSE)

3.4 Plot

plotAnnoBar(peakAnnoList)

plotDistToTSS(peakAnnoList)

pdf('results/Features/Hep.Myo.Bcell-specificANDstable-CTCF-GenomciAnnotation-barplot.pdf', width = 5, height = 3)
plotAnnoBar(peakAnnoList)
plotDistToTSS(peakAnnoList)
dev.off()