Generates a WIG file containing the coverage values for a certain genomic interval

Description

Write the coverage values calculated using the cov.interval function into a WIG format file

Usage

## S4 method for signature 'numeric'
export.wig(cov,outfile=NULL)

Arguments

Details

This method is used to write the coverage values calculated by the cov.interval function into a WIG format file.

Author(s)

Ernesto Lowy <ernestolowy@gmail.com>

References

WIG format specification: https://genome.ucsc.edu/FAQ/FAQformat.html

See Also

cov.interval

Examples

#get treatment and control test files
treat1file<-system.file("extdata","treat.bam",package="CoverageView")
control1file<-system.file("extdata","ctrl.bam",package="CoverageView")
  
#create two CoverageBamFile objects representing single-end alignments
trm1<-CoverageBamFile(treat1file,run_type="single")
ctl1<-CoverageBamFile(control1file,run_type="single")
  
#calculate the ratio of the coverages for the defined genomic interval using a bin_width equal to 10 nts
cov1=cov.interval(trm1,ctl1,chr="chrI",start=1,end=100,bin_width=10,do="ratio")
  
#create a WIG file with the obtained vector with the ratios
outfolder=system.file("extdata",package="CoverageView")
an_outfile1=paste(outfolder,"out.wig",sep="/")
export.wig(cov1,outfile=an_outfile1)

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)

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> library(CoverageView)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
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

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer

Attaching package: 'CoverageView'

The following object is masked from 'package:rtracklayer':

    export.wig

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/CoverageView/export.wig.Rd_%03d_medium.png", width=480, height=480)
> ### Name: export.wig
> ### Title: Generates a WIG file containing the coverage values for a
> ###   certain genomic interval
> ### Aliases: export.wig export.wig,numeric-method
> 
> ### ** Examples
> 
> #get treatment and control test files
> treat1file<-system.file("extdata","treat.bam",package="CoverageView")
> control1file<-system.file("extdata","ctrl.bam",package="CoverageView")
>   
> #create two CoverageBamFile objects representing single-end alignments
> trm1<-CoverageBamFile(treat1file,run_type="single")
> ctl1<-CoverageBamFile(control1file,run_type="single")
>   
> #calculate the ratio of the coverages for the defined genomic interval using a bin_width equal to 10 nts
> cov1=cov.interval(trm1,ctl1,chr="chrI",start=1,end=100,bin_width=10,do="ratio")
>   
> #create a WIG file with the obtained vector with the ratios
> outfolder=system.file("extdata",package="CoverageView")
> an_outfile1=paste(outfolder,"out.wig",sep="/")
> export.wig(cov1,outfile=an_outfile1)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>