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

## Documentation for package ‘CNTools’ version 1.2.0

## User Guides and Package Vignettes

Read overview or 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,ANY-method | A filter that filters out features that do not differ by a set threshold between a pair of samples
diffBy,RS-method | 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,RS-method | ~~ Methods for Function genefilter ~~
genefilter-methods | ~~ Methods for Function genefilter ~~
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,ANY-method | Method that extends the cor function of stats to handle reduced segment data
getCor,RS-method | 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,ANY-method | A method that extends the generic function dist to handle reduced segemnts
getDist,RS-method | 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,CNSeg-method | 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,ANY-method | Method that filters reduced segment matrix by the mean absolute deviation
madFilter,RS-method | 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,RS-method | 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<- | Class "RS" contains the Reduced Segment data matrix derived from the output of segmentation
rs<-,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,RS-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,CNSeg-method | 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<-,CNSeg-method | Class "CNSeg" contains the output of DNACopy segmentation data that can be operated on by the associated methods
show,CNSeg-method | Class "CNSeg" contains the output of DNACopy segmentation data that can be operated on by the associated methods
show,RS-method | Class "RS" contains the Reduced Segment data matrix derived from the output of segmentation