write.profile: Write coverage values into a file
In CoverageView: Coverage visualization package for R

Description Usage Arguments Details Author(s) See Also Examples

Write the coverage values calculated using the cov.matrix function into a file

1 2	## S4 method for signature 'matrix' write.profile(DF,outfile=NULL)

`DF`	Coverage matrix generated by the function `cov.matrix`
`outfile`	Where to write the `.txt` file that will contain the matrix

This method is used to write the matrix containing the coverage values calculated by cov.matrix into a file.

Ernesto Lowy <ernestolowy@gmail.com>

cov.matrix

#get a BAM test file
treatBAMfile<-system.file("extdata","treat.bam",package="CoverageView")
  
#get a BED file with the TSS (transcription start site) coordinates of some genes
bedfile<-system.file("extdata","testTSS.bed",package="CoverageView")
  
#create the CoverageBamFile object
trm<-CoverageBamFile(treatBAMfile)
  
#generate the coverage matrix extending 100 nts on each side of the TSS provided
#in the BED file
DF1=cov.matrix(trm,coordfile=bedfile,extend=100)
  
#write the coverage matrix into the provided file
write.profile(DF1,outfile="DF1.txt")