peaksCAT {gcapc} | R Documentation

## CATplot of Peaks

### 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))

[Package gcapc version 1.12.0 Index]