CoverageBigWigFile-class: Class '"CoverageBigWigFile"'

In CoverageView: Coverage visualization package for R

Description

The CoverageBigWigFile class contains information on a BigWIG file and inherits fields from the BigWigFile class in the rtracklayer package.

Objects from the Class

Objects can be created by calls of the form CoverageBigWigFile(). This class represents an alignment in the BigWIG format for which each genomic position has a depth of coverage value associated.

The reads_mapped argument is optional but it is required if the normalization parameter is set in the cov.matrix and cov.interval functions

Slots

resource

A character string that details the path to the BigWIG file

reads_mapped

A number representing the number of reads aligned in the file. Default = 0

...

Additional arguments

Author(s)

Ernesto Lowy <[e-mail]>

References

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

See Also

• BigWigFile

• CoverageBamFile

Examples

##get BigWIG test file
inputfile<-system.file("extdata","treat.bw",package="CoverageView")

#create a CoverageBigWigFile object
trm<-CoverageBigWigFile(inputfile)

#create a CoverageBigWigFile object including the information of the number of reads aligned
trm1<-CoverageBigWigFile(inputfile,reads_mapped=28654321)

##get BigWIG test file
inputfile<-system.file("extdata","treat.bw",package="CoverageView")

#create a CoverageBigWigFile object
trm<-CoverageBigWigFile(inputfile)

#create a CoverageBigWigFile object including the information of the number of reads aligned
trm1<-CoverageBigWigFile(inputfile,reads_mapped=28654321)

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