methylKit (version 0.99.2)

diffMethPerChr: Get and plot the number of hyper/hypo methylated regions/bases per chromosome

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 = TRUE, qvalue.cutoff = 0.01, meth.cutoff = 25,
  exclude = NULL, ...)
# S4 method for methylDiff
diffMethPerChr(x, plot = TRUE, qvalue.cutoff = 0.01,
  meth.cutoff = 25, exclude = NULL, ...)
# S4 method for methylDiffDB
diffMethPerChr(x, plot = TRUE,
  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

# NOT RUN {
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)

# }