Annotation with ChIPpeakAnno package

The following annotates the identified peaks with genomic context information using the ChIPpeakAnno and ChIPseeker packages, respectively (Zhu et al., 2010; Yu et al., 2015).

library(ChIPpeakAnno); library(GenomicFeatures)
args <- systemArgs(sysma="param/annotate_peaks.param", mytargets="targets_macs.txt")
# txdb <- loadDb("./data/tair10.sqlite")
txdb <- makeTxDbFromGFF(file="data/tair10.gff", format="gff", dataSource="TAIR", organism="Arabidopsis thaliana")
ge <- genes(txdb, columns=c("tx_name", "gene_id", "tx_type")) 
for(i in seq(along=args)) {
    peaksGR <- as(read.delim(infile1(args)[i], comment="#"), "GRanges")
    annotatedPeak <- annotatePeakInBatch(peaksGR, AnnotationData=genes(txdb))
    df <- data.frame(as.data.frame(annotatedPeak), as.data.frame(values(ge[values(annotatedPeak)$feature,])))
    write.table(df, outpaths(args[i]), quote=FALSE, row.names=FALSE, sep="\t")
}
writeTargetsout(x=args, file="targets_peakanno.txt", overwrite=TRUE)

The peak annotation results are written for each peak set to separate files in the results directory. They are named after the corresponding peak files with extensions specified in the annotate_peaks.param file, here *.peaks.annotated.xls.

Annotation with ChIPseeker package

Same as in previous step but using the ChIPseeker package for annotating the peaks.

library(ChIPseeker)
for(i in seq(along=args)) {
    peakAnno <- annotatePeak(infile1(args)[i], TxDb=txdb, verbose=FALSE)
    df <- as.data.frame(peakAnno)
    write.table(df, outpaths(args[i]), quote=FALSE, row.names=FALSE, sep="\t")
}
writeTargetsout(x=args, file="targets_peakanno.txt", overwrite=TRUE)

Summary plots provided by the ChIPseeker package. Here applied only to one sample for demonstration purposes.

peak <- readPeakFile(infile1(args)[1])
covplot(peak, weightCol="X.log10.pvalue.")
peakHeatmap(outpaths(args)[1], TxDb=txdb, upstream=1000, downstream=1000, color="red")
plotAvgProf2(outpaths(args)[1], TxDb=txdb, upstream=1000, downstream=1000, xlab="Genomic Region (5'->3')", ylab = "Read Count Frequency")



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