export.wig: Generates a WIG file containing the coverage values for a...
In CoverageView: Coverage visualization package for R

Description Usage Arguments Details Author(s) References See Also Examples

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

1 2	## S4 method for signature 'numeric' export.wig(cov,outfile=NULL)

`cov`	Numeric vector containing the coverage values generated by the function `cov.interval`
`outfile`	Where to write the `.WIG` format file that will contain the coverages

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

Ernesto Lowy <ernestolowy@gmail.com>

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

cov.interval

#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)