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Jit

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Generates a genome coverage plot with R

Jit
  • Public
By Jit 2048 days ago Comments (1)
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")

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