diffMethPerChr-methods: Get and plot the number of hyper/hypo methylated...

In vd4mmind/methylkit: DNA methylation analysis from high-throughput bisulfite sequencing results

Description

This function gets number of hyper/hypo methylated regions/bases from methylDiff object. It can also plot percentages of differentially methylated bases per chromosome.

Usage

  diffMethPerChr(x,plot=T,qvalue.cutoff=0.01,
    meth.cutoff=25,exclude=NULL,...)

Arguments

x	a methylDiff object
plot	TRUE|FALSE. If TRUE horizontal barplots for proportion of hypo/hyper methylated bases/regions
qvalue.cutoff	cutoff for q-value
meth.cutoff	cutoff for percent methylation difference
exclude	names of chromosomes to be excluded
...	extra graphical parameters to be passed to barplot function

Value

plots a piechart or a barplot for percentage of the target features overlapping with annotation

Examples

data(methylKit)

# get a list of differentially methylated bases/regions per chromosome and overall
diffMethPerChr(methylDiff.obj, plot=FALSE,qvalue.cutoff=0.01, meth.cutoff=25,exclude=NULL)

vd4mmind/methylkit documentation built on May 3, 2019, 4:57 p.m.