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 |
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
1 2 3 4 5 6 | 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")
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