Generates a cumulative genome coverage plot

Description

This method generates a plot showing the percentage of the genome covered at different read depths

Usage

  ## S4 method for signature 'CoverageBamFile'
genome.covplot.cumdepth(data,outfile,max_depth)
  ## S4 method for signature 'list'
genome.covplot.cumdepth(data,outfile,max_depth)

Arguments

Details

This method receives either a single CoverageBamFile object or a list of CoverageBamFile objects and generates a plot for which the X-axis is a range of cumulative read depths and the Y-axis is the percentage of the genome covered at a certain read depth. If a list of CoverageBamFile objects is passed to the function then it will generate a different coloured line for each of the passed objects

Author(s)

Ernesto Lowy <ernestolowy@gmail.com>

See Also

genome.covplot.depth

Examples

##draw a cumulative coverage plot for a test case BAM file
  
#get a BAM test file
treatBAMfile<-system.file("extdata","treat.bam",package="CoverageView")
  
#create a CoverageBamFile object
trm<-CoverageBamFile(treatBAMfile)
  
#draw the plot
genome.covplot.cumdepth(trm,outfile="test.png")
  
#draw the plot setting the max_depth parameter (30X in this case)
genome.covplot.cumdepth(trm,outfile="test.png",max_depth=30)
  
##draw two overlapping cumulative coverage plots for two different BAM files
  
#get the first BAM file
treatBAMfile<-system.file("extdata","treat.bam",package="CoverageView")
#create the CoverageBamFile object
trm<-CoverageBamFile(treatBAMfile)
  
#get the second BAM test file
ctrlBAMfile<-system.file("extdata","ctrl.bam",package="CoverageView")
#create the CoverageBamFile object
ctl<-CoverageBamFile(ctrlBAMfile)

#create a list with the two files
input_d=list(trm,ctl)
  
#draw the plot
genome.covplot.cumdepth(input_d,outfile="test.png")

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/genome.covplot.cumdepth.Rd_%03d_medium.png", width=480, height=480)
> ### Name: genome.covplot.cumdepth
> ### Title: Generates a cumulative genome coverage plot
> ### Aliases: genome.covplot.cumdepth
> ###   genome.covplot.cumdepth,CoverageBamFile-method
> ###   genome.covplot.cumdepth,list-method
> 
> ### ** Examples
> 
> ##draw a cumulative coverage plot for a test case BAM file
>   
> #get a BAM test file
> treatBAMfile<-system.file("extdata","treat.bam",package="CoverageView")
>   
> #create a CoverageBamFile object
> trm<-CoverageBamFile(treatBAMfile)
>   
> #draw the plot
> genome.covplot.cumdepth(trm,outfile="test.png")
png 
  2 
>   
> #draw the plot setting the max_depth parameter (30X in this case)
> genome.covplot.cumdepth(trm,outfile="test.png",max_depth=30)
png 
  2 
>   
> ##draw two overlapping cumulative coverage plots for two different BAM files
>   
> #get the first BAM file
> treatBAMfile<-system.file("extdata","treat.bam",package="CoverageView")
> #create the CoverageBamFile object
> trm<-CoverageBamFile(treatBAMfile)
>   
> #get the second BAM test file
> ctrlBAMfile<-system.file("extdata","ctrl.bam",package="CoverageView")
> #create the CoverageBamFile object
> ctl<-CoverageBamFile(ctrlBAMfile)
> 
> #create a list with the two files
> input_d=list(trm,ctl)
>   
> #draw the plot
> genome.covplot.cumdepth(input_d,outfile="test.png")
png 
  2 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>