CNGEheatmaps: Parellel CN and GE heatmap plotting

Description Usage Arguments Details Author(s) References See Also Examples

View source: R/plotFunctions.r

Description

Heatmaps of DNA copy number and gene expression data are plotted together.

Usage

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CNGEheatmaps(CNdata, GEdata, location = "mode", colorbreaks = "equiquantiles")

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).

location

Parameter (median, mean, or mode) specifying how the center of the gene expression heatmap color-scheme is determined.

colorbreaks

Parameter specifying how the color distribution of the gene expression heatmap is determined, either equiquantiles or equidistant.

Details

The DNA copy number data heatmap is generated as follows. The DNA copy number data are used to determine the genomic segments exhibiting no difference in DNA copy number between the array elements that map to that segment. This resembles the dimension reduction technique employed in the CGHregions-package. Consequently, within a segment the DNA copy number for one sample is constant, but may vary between samples. Note that a region may comprise of a whole chromosome, but also of a focal amplication. It is the DNA copy number signature of the segments that is depicted in the heatmap of the DNA copy number data.

For the gene expression heatmap segments as constructed for the array CGH data are adopted. For each segment-sample combination the expression levels of the genes that map to that segment are averaged. Next, the gene expression data is also collapsed to the segment format. It is this collapsed and averaged expression data that is depicted in the corresponding heatmap.

Author(s)

Wessel N. van Wieringen: [email protected]

References

Van de Wiel, M.A., Van Wieringen, W.N. (2007), "CGHregions: dimension reduction for array CGH data with minimal information loss", Cancer Informatics, 2, 55-63.

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

cghCall, ExpressionSet, matchCGHcall2ExpressionSet, profilesPlot,

Examples

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# load data
data(pollackCN16) 
data(pollackGE16) 

# plot heatmaps
CNGEheatmaps(pollackCN16, pollackGE16, location = "mode", colorbreaks = "equiquantiles") 

sigaR documentation built on May 6, 2019, 3:40 a.m.