plotDistro: plotDistro

In ssviz: A small RNA-seq visualizer and analysis toolkit

Description

Plots distribution of reads in the bam file based on length, direction (strand) or location (rname)

Usage

plotDistro(bamlist, type = "qwidth", samplenames = NULL, unique = FALSE, ncounts = NULL, norm = FALSE, yname = "Counts per million")

Arguments

bamlist	An object of type list, giving a list of bam files. If you only have 1 file, use list(bam_file)
type	An object of type character. Can be qwidth,rname or strand. In theory, any column property existing in the bam file can be used, but these 3 would be most meaningful.
samplenames	Labels for the plot.
unique	Logical value to use unique reads (TRUE) or all reads (FALSE)
ncounts	Number of total counts in the bam file, used if unique is set to FALSE.
norm	Logical value to determine if plot will be normalised.
yname	y axis label.

Author(s)

Diana H.P. Low

Examples

data(ssviz)
plotDistro(list(ctrlbam))

ssviz documentation built on Nov. 8, 2020, 5:53 p.m.