methylKit (version 0.9.5)

getCoverageStats: get coverage stats from methylRaw object

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

# NOT RUN {
data(methylKit)

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