cov.interval: arithmetic operation on an interval
In CoverageView: Coverage visualization package for R

Description Usage Arguments Details Author(s) References Examples

This method computes a numeric vector with the result of a certain arithmetic operation with the coverage for two particular BAM or BigWIG files within a specific genomic interval defined by the user

  ## S4 method for signature 'CoverageBamFile,CoverageBamFile'
cov.interval(tr,ctl,normalization,chr,start,end,bin_width,do)
  ## S4 method for signature 'CoverageBigWigFile,CoverageBigWigFile'
cov.interval(tr,ctl,normalization,chr,start,end,bin_width,do)

`tr`	An instance of a `CoverageBamFile` or a `CoverageBigWigFile` object used to compute an arithmetic operation with the coverage values for the genomic interval defined by the `chr`, `start` and `end` parameters
`ctl`	An instance of a `CoverageBamFile` or a `CoverageBigWigFile` object used to compute a certain arithmetic operation with the coverage values for the genomic interval defined by the `chr`, `start` and `end` parameters
`normalization`	Normalize the coverage values in the resulting numeric vector. Possible normalization types are `rpm` (Read per million). Default=NULL
`chr`	chromosome of the genomic interval
`start`	start coordinate of the genomic interval. If the `start` and `end` arguments are not set, then the entire chromosome defined with the `chr` argument will be used for the calculations
`end`	end coordinate of the genomic interval
`bin_width`	calculate the average coverage within bins of size defined by this argument. Default is 1 nucleotide
`do`	specify the arithmetic operation to perform on the genomic interval. Possible values are 'log2ratio','ratio' or 'substraction'.Default=`log2ratio`

The cov.interval function receives 2 CoverageBamFiles or CoverageBigWigFiles objects and returns a numeric vector with the result of doing a certain arithmetic operation with the two files using the coverage values for a certain position or genomic bin that is included in the genomic interval defined by the user using the chr, start and end arguments. The size of the bins is controlled by the bin_width argument and for each bin the average coverage value is computed and used for the different arithmetic operations.The arithmetic operation to perform is set with the do argument.

If the normalization parameter is set to 'rpm' then the number of reads aligned into the reference is required to perform the normalization. This number can be provided using the reads_mapped argument of the CoverageBamFile or CoverageBigWigFile objects, or it is automatically calculated if the function is used with a CoverageBamFile object. NOTE: If the reads_mapped argument is set then the automatic calculation will NOT be performed and the provided number will be taken as correct for all downstream calculations.

Ernesto Lowy <ernestolowy@gmail.com>

BAM format specification: http://samtools.sourceforge.net/SAMv1.pdf

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

##BAM files
  
#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)
  
##BigWIG files
  
#get a treatment and control test files
treat2file<-system.file("extdata","treat.bw",package="CoverageView")
control2file<-system.file("extdata","ctrl.bw",package="CoverageView")
  
#create the 'treatment' and 'control' CoverageBigWigFile objects
trm2<-CoverageBigWigFile(path=treat2file,reads_mapped=28564510)
ctl2<-CoverageBigWigFile(path=control2file,reads_mapped=26713667)
  
#calculate the ratio of the coverages for the defined genomic interval
cov2=cov.interval(trm2,ctl2,bin_width=1,chr="chrI",start=1,end=1000,do='ratio')