peaksCAT: CATplot of Peaks

In gcapc: GC Aware Peak Caller

Description

Plot the consistancy between two peak lists by their significance.

Usage

peaksCAT(x, y, ranks = seq(200, min(length(x), length(y), 20000), 50),
  exclude = GRanges(), seqinfo = NULL, esx = 1, esy = 1, add = FALSE,
  ...)

Arguments

x	A GRanges of identified peaks from one method or one replicate. At least one meta column should be included to allow for significance ranking of peaks.
y	A GRanges of identified peaks from compared method or anoter replicate. At least one meta column should be included to allow for significance ranking of peaks.
ranks	A non-negative integer vector specifying the ranks to be used for CAT plot.
exclude	A GRanges object specifying regions to be excluded for CAT plot, such as the blacklist regions proposed by ENCODE Consortium.
seqinfo	A vector of chromosome names to limit the CAT plot to selected chromosomes. Chromosome names here must be in the same format as seqnames in x and y. This parameter also helps exclude uncommon chromosomes, e.g. using value paste0('chr',c(1:22,'X','Y')) for human genome. Default: NULL means no limit to chromosomes.
esx	A non-negative integer specifying which meta column of x to be used to rank peak significance. Larger values in this column should indicate higher significance.
esy	A non-negative integer specifying which meta column of y to be used to rank peak significance. Larger values in this column should indicate higher significance.
add	A logical vector which, when TRUE, adds the current plotting line to existing plots. FALSE will generate a new plot.
...	Other parameters passed to plot or lines.

Value

A CAT plot.

Examples

bam <- system.file("extdata", "chipseq.bam", package="gcapc")
cov <- read5endCoverage(bam)
bdw <- bindWidth(cov)
gcb1 <- gcEffects(cov, bdw, sampling=c(0.15,1), plot=FALSE)
peaks1 <- gcapcPeaks(cov, gcb1, bdw)
gcb2 <- gcEffects(cov, bdw, sampling=c(0.2,1), plot=FALSE)
peaks2 <- gcapcPeaks(cov, gcb2, bdw)
peaksCAT(peaks1, peaks2, ranks=seq(100,200,5), ylim=c(0,1))

gcapc documentation built on Nov. 8, 2020, 8:14 p.m.