CoverageView (version 1.8.0)

genome.covplot.cumdepth: Generates a cumulative genome coverage plot

Description

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

Usage

"genome.covplot.cumdepth"(data,outfile,max_depth) "genome.covplot.cumdepth"(data,outfile,max_depth)

Arguments

data

Either an instance of CoverageBamFile or a list of CoverageBamFile objects

outfile

URL of the .png file where the plot will be created

max_depth

Maximum read depth to be displayed in the X-axis

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

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")