MEDIPS (version 1.22.0)

MEDIPS.addCNV: Function to run a copy number variation analysis.

Description

Function calculates a CNV analysis based on two INPUT SETs by employing the DNAcopy package. The results are attached to a provided result table.

Usage

MEDIPS.addCNV(ISet1, ISet2, results, cnv.Frame=1000)

Arguments

ISet1

First group of INPUT SETs

ISet2

Second group of INPUT SETs

results

result table as returned by the MEDIPS.meth function

cnv.Frame

window size used for calculating CNVs. Can be of different size than the result table.

Value

The result table with an additional column containing DNAcopy's log-ratio.

Examples

library(MEDIPSData)
library("BSgenome.Hsapiens.UCSC.hg19")

bam.file.hESCs.Input = system.file("extdata", "hESCs.Input.chr22.bam", package="MEDIPSData")
bam.file.DE.Input = system.file("extdata", "DE.Input.chr22.bam", package="MEDIPSData")

hESCs.Input = MEDIPS.createSet(file=bam.file.hESCs.Input, BSgenome="BSgenome.Hsapiens.UCSC.hg19", extend=250, shift=0, uniq=1e-3, window_size=100, chr.select="chr22")
DE.Input = MEDIPS.createSet(file=bam.file.DE.Input, BSgenome="BSgenome.Hsapiens.UCSC.hg19", extend=250, shift=0, uniq=1e-3, window_size=100, chr.select="chr22")

data(resultTable)

resultTable = MEDIPS.addCNV(cnv.Frame=10000, ISet1=hESCs.Input, ISet2=DE.Input, results=resultTable)