bedgraph {methylKit} | R Documentation

## Get bedgraph from methylRaw, methylRawList and methylDiff objects

### Description

The function converts `methylRaw`, `methylRawDB`, `methylRawList`, `methylRawListDB`, `methylDiff` or `methylDiffDB` object into a bedgraph format. It either writes as a file or returns a `data.frame`

### Usage

    bedgraph(
      methylObj,
      file.name = NULL,
      col.name,
      unmeth = FALSE,
      log.transform = FALSE,
      negative = FALSE,
      add.on = "",
      chunk.size = 1e+06
    )

    ## S4 method for signature 'methylDiff'
    bedgraph(
      methylObj,
      file.name,
      col.name,
      unmeth,
      log.transform,
      negative,
      add.on
    )

    ## S4 method for signature 'methylRaw'
    bedgraph(
      methylObj,
      file.name,
      col.name,
      unmeth,
      log.transform,
      negative,
      add.on
    )

    ## S4 method for signature 'methylRawList'
    bedgraph(
      methylObj,
      file.name,
      col.name,
      unmeth,
      log.transform,
      negative,
      add.on
    )

    ## S4 method for signature 'methylRawDB'
    bedgraph(
      methylObj,
      file.name = NULL,
      col.name,
      unmeth = FALSE,
      log.transform = FALSE,
      negative = FALSE,
      add.on = "",
      chunk.size = 1e+06
    )

    ## S4 method for signature 'methylRawListDB'
    bedgraph(
      methylObj,
      file.name = NULL,
      col.name,
      unmeth = FALSE,
      log.transform = FALSE,
      negative = FALSE,
      add.on = "",
      chunk.size = 1e+06
    )

    ## S4 method for signature 'methylDiffDB'
    bedgraph(
      methylObj,
      file.name,
      col.name,
      log.transform,
      negative,
      add.on,
      chunk.size
    )

### Arguments

`methylObj` | a `methylRaw`, `methylRawDB`, `methylRawList`, `methylRawListDB`, `methylDiff` or `methylDiffDB` object
`file.name` | Default: NULL. if a string is given a bedgraph file will be written, if NULL a data.frame or a list of data frames will be returned
`col.name` | name of the column in `methylRaw`, `methylRawDB`, `methylRawList`, `methylRawListDB`, `methylDiff` or `methylDiffDB` objects to be used as a score for the bedgraph. For `methylDiff` or `methylDiffDB`, `col.name` must be one of the following 'pvalue','qvalue', 'meth.diff'. For `methylRaw`, `methylRawDB`, `methylRawList` and `methylRawListDB` it must be one of the following 'coverage', 'numCs','numTs', 'perc.meth'
`unmeth` | when working with `methylRaw`, `methylRawDB`, `methylRawList` and `methylRawListDB` objects should you output unmethylated C percentage this makes it easier to see the unmethylated bases because their methylation percentage values will be zero. Only invoked when file.name is not NULL.
`log.transform` | Default FALSE, If TRUE the score column of the bedgraph wil be in log10 scale. Ignored when col.name='perc.meth'
`negative` | Default FALSE, If TRUE, the score column of the bedgraph will be multiplied by -1. Ignored when col.name='perc.meth'
`add.on` | additional string to be add on the track line of bedgraph. can be viewlimits,priority etc. Check bedgraph track line options at UCSC browser
`chunk.size` | Number of rows to be taken as a chunk for processing the `methylRawDB`, `methylRawListDB` or `methylDiffDB` objects, default: 1e6

### Value

Returns a `data.frame` or list of data.frames if `file.name=NULL`, if a file.name given appropriate bed file will be written to that file

### Details

The parameter `chunk.size` is only used when working with `methylRawDB`, `methylRawListDB` or `methylDiffDB` 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)

    # getting a bedgraph file from a methylDiff object containing differential
    # methylation percentages
    bedgraph(methylDiff.obj, file.name="test.bed", col.name="meth.diff",
             unmeth=FALSE,log.transform=FALSE,negative=FALSE,add.on="")

    # remove the file
    unlink("test.bed")

    # getting a bedgraph file from a methylBase object containing percent
    #methylation values
    bedgraph(methylRawList.obj[[1]], file.name="test2.bed", col.name="perc.meth",
             unmeth=FALSE,log.transform=FALSE,negative=FALSE,add.on="")

    unlink("test2.bed") # remove the file

[Package methylKit version 1.18.0 Index]