MEDIPS.exportWIG: Exports count, rpkm, or sequence pattern densities into a...
In chavez-lab/MEDIPS: DNA IP-seq data analysis

Description Usage Arguments Value Author(s) Examples

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.

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

`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.

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

Lukas Chavez

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")