MEDIPS (version 1.22.0)

MEDIPS.exportWIG: Exports count, rpkm, or sequence pattern densities into a wiggle file.

Description

The function allows for exporting the calculated methylation values (counts or rpkm) or sequence pattern densities from a MEDIPS or COUPLING SET into a wiggle (WIG) file. The wiggle file will contain values for all genomic windows of the genome/coupling vector and can be used for data visualization using appropriate genome browsers. Either a MEDIPS SET (parameter MSet) or a COUPLING SET (parameter CSet) has to be given.

Usage

MEDIPS.exportWIG(Set=NULL, CSet=NULL, file=NULL, format="rpkm", descr="")

Arguments

Set

has to be a MEDIPS SET object. Required when the parameter 'format' is 'count', 'rpkm', or 'rms'.

CSet

has to be a COUPLING SET object. Required when the parameter 'format' is 'pdensity' or 'rms'.

file

defines the name of the exported file

format

if set to "count", there must be a MEDIPS SET at 'Set'. The number of overlapping (extended) short reads per window will be exported. if set to "rpkm", there must be a MEDIPS SET at 'Set'. The rpkm values will be exported (default). If set to "pdensity", there must be a COUPLING SET at 'CSet'. The pattern densities (counts per window) will be exported (parameter Set will be ignored). If set to 'rms', there must be a MEDIPS SET at 'Set' and a corresponding COUPLING SET at 'CSet'. The CpG density normalized methylatin estimates will be exported.

descr

the exported wiggle file will include a track name and description that will be visualized by the utilized genome browser. Both, track name and description will be the same as defined here.

Value

the funtion exports the specified data from the MEDIPS or COUPLING SET into the stated file

Examples

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

bam.file.hESCs.Rep1.MeDIP = system.file("extdata", "hESCs.MeDIP.Rep1.chr22.bam", package="MEDIPSData")
MSet=MEDIPS.createSet(file=bam.file.hESCs.Rep1.MeDIP, BSgenome="BSgenome.Hsapiens.UCSC.hg19", chr.select="chr22", extend=250, shift=0, uniq=1e-3)

MEDIPS.exportWIG(Set=MSet, file="hESCs.Rep1.wig", format="rpkm", descr="hESCs.Rep1")