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

## Documentation for package ‘CNTools’ version 1.4.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

CNSeg | Class "CNSeg" contains the output of DNACopy segmentation data that can be operated on by the associated methods
CNSeg-class | Class "CNSeg" contains the output of DNACopy segmentation data that can be operated on by the associated methods
diffBy | A filter that filters out features that do not differ by a set threshold between a pair of samples
diffBy-method | A filter that filters out features that do not differ by a set threshold between a pair of samples
genefilter-method | A method that filters feature based on reduced segment
genefilter-methods | A method that filters feature based on reduced segment
geneInfo | method that convert segment data into reduced segment matrix
getCor | Method that extends the cor function of stats to handle reduced segment data
getCor-method | Method that extends the cor function of stats to handle reduced segment data
getDist | A method that extends the generic function dist to handle reduced segemnts
getDist-method | A method that extends the generic function dist to handle reduced segemnts
getRS | method that convert segment data into reduced segment matrix
getRS-method | method that convert segment data into reduced segment matrix
madFilter | Method that filters reduced segment matrix by the mean absolute deviation
madFilter-method | Method that filters reduced segment matrix by the mean absolute deviation
rs | Class "RS" contains the Reduced Segment data matrix derived from the output of segmentation
RS-class | Class "RS" contains the Reduced Segment data matrix derived from the output of segmentation
rs-method | Class "RS" contains the Reduced Segment data matrix derived from the output of segmentation
rs<- | Class "RS" contains the Reduced Segment data matrix derived from the output of segmentation
rs<--method | Class "RS" contains the Reduced Segment data matrix derived from the output of segmentation
sampleData | Class "CNSeg" contains the output of DNACopy segmentation data that can be operated on by the associated methods
segBy | Class "RS" contains the Reduced Segment data matrix derived from the output of segmentation
segBy-method | Class "RS" contains the Reduced Segment data matrix derived from the output of segmentation
segList | Class "CNSeg" contains the output of DNACopy segmentation data that can be operated on by the associated methods
segList-method | Class "CNSeg" contains the output of DNACopy segmentation data that can be operated on by the associated methods
segList<- | Class "CNSeg" contains the output of DNACopy segmentation data that can be operated on by the associated methods
segList<--method | Class "CNSeg" contains the output of DNACopy segmentation data that can be operated on by the associated methods
show-method | Class "CNSeg" contains the output of DNACopy segmentation data that can be operated on by the associated methods
show-method | Class "RS" contains the Reduced Segment data matrix derived from the output of segmentation