Class "CoverageBigWigFile"

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 <ernestolowy@gmail.com>

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(CoverageView)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer

Attaching package: 'CoverageView'

The following object is masked from 'package:rtracklayer':

    export.wig

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/CoverageView/CoverageBigWigFile-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CoverageBigWigFile-class
> ### Title: Class '"CoverageBigWigFile"'
> ### Aliases: CoverageBigWigFile-class CoverageBigWigFile
> ###   show,CoverageBigWigFile-method
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>