plotSummaryNumbers: Plot Summary Numbers

In mcjmigdal/sumsamstats: Summarizing Samtools Stats Output With ATAC-seq QC in mind

Description

plotSummaryNumbers plots properties from Summary Numbers (SN) part of output returned by readSamtoolsStats. This includes number of mapped reads, mapped and paired reads, and alignment rate (see details for compleate list). Function also provides means to plot some properties that are not explicitly available in the output.

Usage

plotSummaryNumbers(data, samples, what = "raw total sequences")

Arguments

data	Summary Numbers (SN) part of output returned by readSamtoolsStats or formated data frame of values to plot.
samples	vector of samples names from data that are required to be plotted.
what	string describing property to plot. Valid choices includes all properties from Summary Numbers (SN) part of output returned by readSamtoolsStats and additionaly 'alignment rate'.

Examples

SN <- readSamtoolsStats(system.file('extdata', 'sample1', package = 'sumsamstats'))
plotSummaryNumbers(data = SN, samples = c('sample1'), what = 'raw total sequences')

mcjmigdal/sumsamstats documentation built on July 11, 2021, 10:47 a.m.