getDepth: Get Read Depth

In VaSP: Quantification and Visualization of Variations of Splicing in Population

Description

Get read depth from a BAM file (in bedgraph format)

Usage

getDepth(x, chrom, start, end)

Arguments

x	path to a BAM file
chrom	chromosome of a region to be searched
start	start position
end	end position

Value

a data.frame in bedgraph file format which can be used as input for plotBedgraph in the SuShi package.

See Also

splicePlot

Examples

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')

VaSP documentation built on Feb. 28, 2021, 2:02 a.m.