234    ◾    Bioinformatics

A line plot provided with confidence interval can also be created. The confidence inter-

val is estimated by resampling the peaks several times without replacement and computing

the average and variance each time.

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

conf = 0.95, resample = 1000)

6.3.6.3  Profile of Peaks along Gene Regions

The average peak profile in the different gene regions across genes will give a clear idea

about the site of the protein–DNA interaction. The “plotPeakProf2()” creates a profile plot

for the peak signal from the TSSs to the transcription termination sites (TTSs).

#Profile of ChIP peaks binding to body regions

plotPeakProf2(peak = peaks1Ranges, upstream = rel(0.2), downstream

= rel(0.2),

conf = 0.95, by = “gene”, type = “body”, nbin = 800, TxDb = txdb,

weightCol = “peaks1$peak”,ignore_strand = F)

FIGURE 6.11  Average profile of ChIP-Seq peaks.