diffMethPerChr {methylKit} | R Documentation

## 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)

[Package methylKit version 1.16.1 Index]