cmds.focal.test: Correlation matrix diagonal segmentation(CMDS) to identify...

In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

Description

Correlation matrix diagonal segmentation(CMDS) to identify recurrent CNV.

Usage

cmds.focal.test(data, out.file, wsize=30, wstep=1, chromosomes=paste("chr",1:22, sep=""))

Arguments

data	A data frame with chromosome, position and CN in each sample.
out.file	Output file.
wsize	Block size.
wstep	Step size.
chromosomes	A vector of chromosomes analyzed.

Details

Qunyuan Zhang et al. CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data Bioinformatics 2010(464-469).

The R source code was downloaded from: https://dsgweb.wustl.edu/qunyuan/software/cmds

See Also

null

Examples

data("cmds")
cmds.focal.test(chr11q, out.file="out.txt", chromosomes="11")

lixiangchun/lxctk documentation built on May 21, 2019, 6:44 a.m.