getDepth {vasp} | R Documentation |
Get read depth from a BAM file (in bedgraph format)
getDepth(x, chrom, start, end)
x |
path to a BAM file |
chrom |
chromosome of a region to be searched |
start |
start position |
end |
end position |
a data.frame in bedgraph file format which can be used as input for
plotBedgraph
in the SuShi package.
path <- system.file('extdata',package='vasp') bam_files<-list.files(path,'bam$') bam_files depth<-getDepth(file.path(path, bam_files[1]), 'Chr1', start=1171800, end=1179400) head(depth) library(Sushi) plotBedgraph(depth,'Chr1',chromstart=1171800, chromend=1179400,yaxt='s') mtext('Depth',side=2,line=2.5,cex=1.2,font=2) labelgenome('Chr1',1171800,1179400,side=1,scipen=20,n=5,scale='Kb')