Generates a genome coverage plot with R

Jit — Wed, 19 Sep 2018 02:44:42 -0500

library(CoverageView)

##draw a coverage plot for a test case BAM file
  
#get a BAM test file
treatBAMfile<-system.file("extdata","treat.bam",package="CoverageView")
  
#create the CoverageBamFile object
trm<-CoverageBamFile(treatBAMfile)
  
#draw the plot
genome.covplot.depth(trm,outfile="test.png")
  
#draw the plot setting the max_depth parameter (70X in this case)
genome.covplot.depth(trm,outfile="test.png",max_depth=70)
  
##draw two overlapping coverage plots for two different test BAM files
  
#get a first BAM test file
treatBAMfile<-system.file("extdata","treat.bam",package="CoverageView")
#create the CoverageBamFile object
trm<-CoverageBamFile(treatBAMfile)
  
#get a 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.depth(input_d,outfile="test.png")

Comment by Jit

Jit — Wed, 19 Sep 2018 02:49:09 -0500

Tutorial at https://bioconductor.org/packages/devel/bioc/vignettes/CoverageView/inst/doc/CoverageView.pdf

BOL: Generates a genome coverage plot with R

Generates a genome coverage plot with R

Comment by Jit