plotProportions {bayesCGH}R Documentation

Plots proportions of gains and losses observed in a set of array CGH data.

Description

Plots proportions of gains and losses observed in a set of array CGH data held in a ClassifySegList object. Proportions of gain are plotted on the positive axis, proportions of loss are plotted on the negative axis. Regions which are frequently gained or lost in the sample set can thus be visually identified.

Usage

plotProportions(seg, arrays, chrom.info = chrominfo.Mb, ylimit=c(-1,1),
                    main="Frequency of genetic changes across tumours", num.chr = 24,
                    amps.dels = TRUE, errors = TRUE, select = FALSE,
                    colors = c("green", "red", "dark green", "dark red"))

Arguments

seg Object of class ClassifySegList.
arrays Which arrays to plot
chrom.info
ylimit Limits on Y-axis. Typically these will be c(-1,1) as this is the maximum range of proportion of loss and gain at any region.
main Title for the plot
num.chr Number of chromosomes to plot; the X and Y chromosomes may be omitted by setting 'num.chr = 22'
amps.dels Plot proportions of amplifications and deletions in addition to proportions of gain and loss.
errors Calculate and plot credibility intervals around proportions. If TRUE, 'amps.dels' is ignored.
select If given, should be a vector identifying the probes to plot
colors The four colors to be used in the plot.

Details

This function plots, for each region along the genome, the proportions of samples in 'seg' showing chromosomal gain (positive) or loss (negative) at that point.

If 'errors = TRUE' then 50% and 90% credibility intervals for the proportions of gain and loss are calculated using an empirical Bayes method with a Dirichlet prior (Hardcastle 2008).

Author(s)

Thomas Hardcastle

References

Hardcastle 2008


[Package bayesCGH version 0.6 Index]