CNGEheatmaps: Parellel CN and GE heatmap plotting
In sigaR: Statistics for Integrative Genomics Analyses in R

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

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

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

`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`.

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.

Wessel N. van Wieringen: w.vanwieringen@vumc.nl

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.

cghCall, ExpressionSet, matchCGHcall2ExpressionSet, profilesPlot,

# load data
data(pollackCN16) 
data(pollackGE16) 

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