getMethylationStats {methylKit} | R Documentation

## get Methylation stats from methylRaw or methylRawDB object

### Description

The function returns basic statistics about It can also plot a histogram of

### Usage

    getMethylationStats(
      object,
      plot = FALSE,
      both.strands = FALSE,
      labels = TRUE,
      ...,
      chunk.size = 1e+06
    )

    ## S4 method for signature 'methylRaw'
    getMethylationStats(
      object,
      plot = FALSE,
      both.strands = FALSE,
      labels = TRUE,
      ...,
      chunk.size = 1e+06
    )

    ## S4 method for signature 'methylRawDB'
    getMethylationStats(
      object,
      plot = FALSE,
      both.strands = FALSE,
      labels = TRUE,
      ...,
      chunk.size = 1e+06
    )

### Arguments

`object` | a `methylRaw` or `methylRawDB` object
`plot` | plot a histogram of Methylation if TRUE (deafult:FALSE)
`both.strands` | do plots and stats for both strands seperately if TRUE (deafult: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.
`chunk.size` | Number of rows to be taken as a chunk for processing the `methylRawDB` objects (default: 1e6)

### Value

a summary of Methylation statistics or plot a histogram of coverage

### Details

The parameter `chunk.size` is only used when working with `methylRawDB` or `methylRawListDB` objects, as they are read in chunk by chunk to enable processing large-sized objects which are stored as flat file database. Per default the chunk.size is set to 1M rows, which should work for most systems. If you encounter memory problems or have a high amount of memory available feel free to adjust the `chunk.size`.

### Examples

    data(methylKit)

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

[Package methylKit version 1.14.2 Index]