Chromatin Immunoprecipitation Sequencing    ◾    233

6.3.6.2  Distribution of Peaks in Transcription Start Site (TSS) Regions

The heatmap can be used to show the peak distribution on the transcription start site (TSS)

region as shown in Figure 6.10.

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

promoter <- getPromoters(TxDb=txdb, upstream=2000,

downstream=2000)

tagMatrix <- getTagMatrix(peaks1Ranges, windows=promoter)

tagHeatmap(tagMatrix, xlim=c(-2000, 2000), color=”blue”)

The distribution of peaks in the TSS region can also be visualized with the line plot that

profiles the average peaks in the TSS region.

plotAvgProf(tagMatrix, xlim=c(-2000, 2000),

xlab=”Genomic Region (5’->3’)”,

ylab = “Read Count Frequency”)

We can notice that as shown in Figure 6.11, the peaks are normally distributed (bell-

shaped) with the mean in the TSS region.

FIGURE 6.10  ChIP-Seq peak profiling in the TSS regions of the genes.