getCoverageStats-methods: get coverage stats from methylRaw object

In fortunatobianconi/methylkit: DNA methylation analysis from high-throughput bisulfite sequencing results

Description

The function returns basic statistics about read coverage per base. It can also plot a histogram of read coverage values.

Usage

  getCoverageStats(object,plot=FALSE,both.strands=FALSE,labels=TRUE,...)

Arguments

object	a methylRaw object
plot	plot a histogram of coverage if TRUE (default:FALSE)
both.strands	do stats and plot for both strands if TRUE (default:FALSE)
labels	should the bars of the histrogram have labels showing the percentage of values in each bin (default:TRUE)
...	options to be passed to hist function

Value

a summary of coverage statistics or plot a histogram of coverage

Examples

data(methylKit)

# gets coverage stats for the first sample in methylRawList.obj object
getCoverageStats(methylRawList.obj[[1]],plot=TRUE,both.strands=FALSE,labels=TRUE)

fortunatobianconi/methylkit documentation built on May 16, 2019, 1:51 p.m.