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Last data update: 2014.03.03

R: Exports count, rpkm, or sequence pattern densities into a...

MEDIPS.exportWIG

R Documentation

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

Author(s)

Lukas Chavez

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")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MEDIPS)
Loading required package: BSgenome
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
Loading required package: Rsamtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MEDIPS/MEDIPS.exportWIG.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MEDIPS.exportWIG
> ### Title: Exports count, rpkm, or sequence pattern densities into a wiggle
> ###   file.
> ### Aliases: MEDIPS.exportWIG
> 
> ### ** 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)
Reading bam alignment hESCs.MeDIP.Rep1.chr22.bam 
Selecting  chr22 
Total number of imported short reads: 152586
Extending reads...
Creating GRange Object...
Keep at most 1 read(s) mapping to the same genomic location
Number of remaining reads: 150793
Calculating genomic coordinates...
Creating Granges object for genome wide windows...
Calculating short read coverage at genome wide windows...
> 
> MEDIPS.exportWIG(Set=MSet, file="hESCs.Rep1.wig", format="rpkm", descr="hESCs.Rep1")
Calculating genomic coordinates...
Creating Granges object for genome wide windows...
Writing data for chr22...
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>