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

In HPCBio/MEDIPS-BioC: DNA IP-seq data 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.

Author(s)

Joern Dietrich

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)

HPCBio/MEDIPS-BioC documentation built on May 30, 2019, 12:44 p.m.