CNTools v1.28.0

by J Zhang

Convert segment data into a region by sample matrix to allow for other high level computational analyses.

This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data

Functions in CNTools

Name Description
RS-class Class "RS" contains the Reduced Segment data matrix derived from the output of segmentation
diffBy-methods A filter that filters out features that do not differ by a set threshold between a pair of samples
getRS-methods method that convert segment data into reduced segment matrix
CNSeg-class Class "CNSeg" contains the output of DNACopy segmentation data that can be operated on by the associated methods
madFilter-methods Method that filters reduced segment matrix by the mean absolute deviation
getCor-methods Method that extends the cor function of stats to handle reduced segment data
genefilter-methods A method that filters feature based on reduced segment
dist-methods A method that extends the generic function dist to handle reduced segemnts
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Keyword copy number
License LGPL
ZipData no
biocViews Microarray, CopyNumberVariation

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