Class "CoverageBamFile"

Description

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

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 <ernestolowy@gmail.com>

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")

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 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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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/CoverageBamFile-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CoverageBamFile-class
> ### Title: Class '"CoverageBamFile"'
> ### Aliases: CoverageBamFile-class CoverageBamFile
> ###   path,CoverageBamFile-method reads_mapped,CoverageBamFile-method
> ###   run_type,CoverageBamFile-method show,CoverageBamFile-method
> ### Keywords: classes
> 
> ### ** 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")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>