sGEmethod: Segmentation of GE data

Description

Segmentation of GE data. This function does the segmentation of both CN and GE data.

Arguments

projectName

String with the name of the project to analyze.

chipTypes

List with the names of both (GE and CN) cdfs.

fncCN

Name of the function to use to summarize the CN data.

Details

The algorithm applies CBS segmentation to both CN and GE data. It also generates a GENESxSAMPLES matrix of CN estimates in order to make it more comparable to GE data.

Value

Returns a list:

matCNsnps

The SNPSxSAMPLES matrix containing segmented CN estimates.

matCNgenes

A GENESxSAMPLES matrix containing segmented CN estimates.

matGEgenes

A GENESxSAMPLES matrix containing segmented GE estimates.

See Also

Check aroma.affymetrix copy number analysis to better understand what is being done here. matrixFromRegions().


Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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