ssviz (version 1.6.2)

plotRegion: plotRegion

Description

Plots the read density given a chromosome region.

Usage

plotRegion(bamlist, region, howsmooth = 2, ncounts = NULL, samplenames = NULL)

Arguments

bamlist

An object of type list, giving a list of bam files. If you only have 1 file, use list(bam_file)

region

An object of type character defining the region to plot. Eg. chr1:1000-2000

howsmooth

Numeric value controlling smoothness of the plot.

ncounts

Total number of reads for plot normalization.

samplenames

Sample names

Value

• Returns the x and y components of the region's reads and plots the density.

Examples

data(ssviz)
region<-'chr1:3015526-3080526'
plotRegion(list(ctrlbam), region=region)