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

In al2na/methylKit: DNA methylation analysis from high-throughput bisulfite sequencing results

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,
  keep.empty.chrom = FALSE,
  ...
)

## S4 method for signature 'methylDiff'
diffMethPerChr(
  x,
  plot = TRUE,
  qvalue.cutoff = 0.01,
  meth.cutoff = 25,
  exclude = NULL,
  keep.empty.chrom = FALSE,
  ...
)

## S4 method for signature 'methylDiffDB'
diffMethPerChr(
  x,
  plot = TRUE,
  qvalue.cutoff = 0.01,
  meth.cutoff = 25,
  exclude = NULL,
  keep.empty.chrom = FALSE,
  ...
)

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 from plot
keep.empty.chrom	keep chromosome in list / plot, even if it contains no hyper/hypo sites
...	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)

al2na/methylKit documentation built on Feb. 1, 2024, 4:42 p.m.