profilesPlot: CN-GE profiles plot

In sigaR: Statistics for Integrative Genomics Analyses in R

Description

Plots a sample's copy number and gene expression data side-by-side. This visualizes the relation between CN and GE within an individual sample.

Usage

profilesPlot(CNdata, GEdata, sampleNo, chr = 0, verbose=TRUE)

Arguments

CNdata	Object of class cghCall, containing (among others) annotion and call probabilities. Features should be matched with those of the accompanying ExpressionSet-object (as may be done using the matchCGHcall2ExpressionSet-function).
GEdata	Object of class ExpressionSet. Features should be matched with those of the accompanying cghCall-object (as may be done using the matchCGHcall2ExpressionSet-function).
sampleNo	Sample number of sample to be plotted. Corresponds to the order in which samples appear the CNdata- and GEdata-objects.
chr	Chromosome number for which the profiles are to be plotted. Default chr=0 for whole genome plotting.
verbose	Logical indicator: should intermediate output be printed on the screen?

Details

The blue lines in the gene expression profile plot are the median expressions of genes that map to the same copy number segment.

Author(s)

Wessel N. van Wieringen: [e-mail]

See Also

cghCall, ExpressionSet

Examples

# load data
data(pollackCN16) 
data(pollackGE16) 

# plot CN and GE profiles alongside
profilesPlot(pollackCN16, pollackGE16, 23, 16) 

sigaR documentation built on April 28, 2020, 6:05 p.m.