copynumber (version 1.12.0)

plotFreq: Plot percentage of samples with an aberration at a genomic position

Description

Plot the percentage of samples that have an amplification or deletion at a genomic position. Amplifications/deletions correspond to copy number values that are above/below a pre-defined threshold. Frequencies may be plotted over the entire genome or separately for each chromosome.

Usage

plotFreq(segments, thres.gain, thres.loss = -thres.gain, pos.unit = "bp",  chrom = NULL, layout = c(1, 1),...)

Arguments

segments

a data frame containing the segmentation results found by either pcf or multipcf.

thres.gain

a numeric vector giving the threshold value(s) to be applied for calling gains.

thres.loss

a numeric vector of same length as thres.gain giving the threshold value(s) to be applied for calling losses. Default is to use the negative value of thres.gain.

pos.unit

the unit used to represent the probe positions. Allowed options are "mbp" (mega base pairs), "kbp" (kilo base pairs) or "bp" (base pairs). By default assumed to be "bp".

chrom

a numeric or character vector with chromosome number(s) to indicate which chromosome(s) is (are) to be plotted. If unspecified the whole genome is plotted, otherwise each specified chromosome is plotted in a separate panel.

layout

an integer vector of length two giving the number of rows and columns in the plot. Default is c(1,1).

...

other graphical parameters. These include the common plot arguments xlab, ylab, title, main, cex.main, mgp, cex.lab, cex.axis, ylim, xlim, and las (see par on these), as well as plot.size, plot.unit, plot.ideo, ideo.frac, cyto.text, assembly and cex.cytotext (see plotSample on these). In addition, some other graphical arguments specific for this plot function may be specified:

col.gain

the color to be used for the gain frequencies, default is "red".

col.loss

the color to be used for the loss frequencies, default is "blue".

continuous

a logical value indicating whether the probe frequencies should be presented as continuous, i.e. the plotted probe frequency will start and end halfway between adjacent probes (except across arms when chromosomes are plotted and except across chromosomes when genome is plotted). Default is TRUE.

percentLines

either a logical value indicating if horizontal percentages lines should be plotted, or a numeric vector with percentages at which such lines should be plotted. Default is TRUE.

Details

The percentage of samples with an aberration is calculated and plotted for all genomic positions. Regions with gain or loss will be those where copy number values are above or below the values given in thres.gain and thres.loss, respectively.

Examples

#load lymphoma data
data(lymphoma)
#Run pcf
seg <- pcf(data=lymphoma,gamma=12)

#Plot over entire genome, gain and loss thresholds are 0.1 and -0.1:
plotFreq(segments=seg,thres.gain=0.1)

#Plot by chromosomes, two sets of thresholds:
plotFreq(segments=seg,thres.gain=c(0.1,0.2), thres.loss=c(-0.05,-0.1), chrom=c(1:23),
layout=c(5,5))