CoverageBamFile-class: Class '"CoverageBamFile"'

In CoverageView: Coverage visualization package for R

Description

The CoverageBamFile class contains information on a BAM file and inherits fields from the BamFile class in the Rsamtools package.

Arguments

path	A character string that details the path to the BAM file
reads_mapped	A number representing the number of reads having an alignment. Default = 0
run_type	A character string describing the type of sequencing run. Possible values are 'single' and 'paired'. Default='single'
...	Additional arguments

Objects from the Class

Use CoverageBamFile() to create a reference to a BAM file.

This class represents an alignment in the BAM format that can be processed by the different methods of the CoverageView package.

The reads_mapped argument is optional and will be automatically calculated (if it is not provided) when the normalization argument is set in the cov.matrix and cov.interval functions

Author(s)

Ernesto Lowy <[e-mail]>

References

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

See Also

• BamFile

• CoverageBigWigFile

Examples

#get a Bam test file
inputfile<-system.file("extdata","treat.bam",package="CoverageView")
  
#create a CoverageBamFile object
trm<-CoverageBamFile(inputfile)
  
#create a CoverageBamFile object including the information of the number
#of reads aligned and the sequencing run type
trm1<-CoverageBamFile(inputfile,reads_mapped=28654321,run_type="single")

CoverageView documentation built on Nov. 8, 2020, 7:52 p.m.