cisEffectPlot: DNA-mRNA plot

In sigaR: Statistics for Integrative Genomics Analyses in R

Description

A variant on the boxplot, plotting the gene expression against the DNA copy number data. For each individual an open blue circle per call is plotted, all with their centerpoint at the height of the individual's expression level. The radius of the circles is proportional to the corresponding call probabilities. Call probabilities equal to zero reduce circles to dots. The red filled circles have a radius proportional to the estimated expected call probabilities, with their centerpoints at the estimated mean expression for the respective call.

Usage

cisEffectPlot(geneId, CNdata, GEdata, verbose=FALSE)

Arguments

geneId	Indicator of the gene to be plotted. Indicator refers to the row in the ExpressionSet-object.
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 matchAnn2Ann-function).
GEdata	Object of class ExpressionSet. Features should be matched with those of the accompanying cghCall-object (as may be done using the matchAnn2Ann-function).
verbose	Logical indicator: should intermediate output be printed on the screen?

Note

This function is a rewritten version of the intCNGEan.plot function of the intCNGEan-package.

Author(s)

Wessel N. van Wieringen: [e-mail]

References

Van Wieringen, W.N., Van de Wiel, M.A. (2009), "Non-parametric testing for DNA copy number induced differential mRNA gene expression", Biometrics, 65(1), 19-29.

See Also

boxplot, cisEffectTune, cisEffectTest, matchAnn2Ann

Examples

# load data
data(pollackCN16)
data(pollackGE16)

# plot DNA copy number vs. gene expression.
cisEffectPlot(225, pollackCN16, pollackGE16)

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