iClusterPlus (version 1.8.0)

CNregions: A function to remove redundant copy number regions

Description

This function is used to reduce copy number regions.

Usage

CNregions(seg, epsilon=0.005, adaptive=FALSE, rmCNV=FALSE, cnv=NULL, frac.overlap=0.5, rmSmallseg=TRUE, nProbes=15)

Arguments

seg

DNAcopy CBS segmentation output.

epsilon

the maximum Euclidean distance between adjacent probes tolerated for denying a nonredundant region. epsilon=0 is equivalent to taking the union of all unique break points across the n samples.

adaptive

Vector of length-m lasso penalty terms.

rmCNV

If TRUE, remove germline CNV.

cnv

A data frame containing germline CNV data.

frac.overlap

A parameter needed to be explain.

rmSmallseg

If TRUE, remove small segment.

nProbes

The segment length threshold below which the segment will be removed if rmSmallseq = TRUE.

Value

A matrix with reduced copy number regions.

References

Qianxing Mo, Sijian Wang, Venkatraman E. Seshan, Adam B. Olshen, Nikolaus Schultz, Chris Sander, R. Scott Powers, Marc Ladanyi, and Ronglai Shen. (2013). Pattern discovery and cancer gene identification in integrated cancer genomic data. Proc. Natl. Acad. Sci. USA.

See Also

breast.chr17,plotiCluster, compute.pod,iCluster,iClusterPlus

Examples

#data(gbm)
#library(GenomicRanges)
#library(cluster)
#reducedM=CNregions(seg,epsilon=0,adaptive=FALSE,rmCNV=TRUE,cnv=NULL,
#  frac.overlap=0.5, rmSmallseg=TRUE,nProbes=5)