tileMethylCounts {methylKit} | R Documentation

## Get methylated/unmethylated base counts for tilling windows

### Description

The function summarizes methylated/unmethylated base counts over tilling windows accross genome. This function can be used when differential methylation analysis is preferable to tilling windows instead of base pairs.

### Usage

    tileMethylCounts(object,win.size=1000,step.size=1000,cov.bases=0,mc.cores=1,save.db,...)

    ## S4 method for signature 'methylRaw'
    tileMethylCounts(
      object,
      win.size = 1000,
      step.size = 1000,
      cov.bases = 0,
      mc.cores = 1,
      save.db = FALSE,
      ...
    )

    ## S4 method for signature 'methylRawList'
    tileMethylCounts(
      object,
      win.size = 1000,
      step.size = 1000,
      cov.bases = 0,
      mc.cores = 1,
      save.db = FALSE,
      ...
    )

    ## S4 method for signature 'methylBase'
    tileMethylCounts(
      object,
      win.size = 1000,
      step.size = 1000,
      cov.bases = 0,
      mc.cores = 1,
      save.db = FALSE,
      ...
    )

    ## S4 method for signature 'methylRawDB'
    tileMethylCounts(
      object,
      win.size = 1000,
      step.size = 1000,
      cov.bases = 0,
      mc.cores = 1,
      save.db = TRUE,
      ...
    )

    ## S4 method for signature 'methylRawListDB'
    tileMethylCounts(
      object,
      win.size = 1000,
      step.size = 1000,
      cov.bases = 0,
      mc.cores = 1,
      save.db = TRUE,
      ...
    )

    ## S4 method for signature 'methylBaseDB'
    tileMethylCounts(
      object,
      win.size = 1000,
      step.size = 1000,
      cov.bases = 0,
      mc.cores = 1,
      save.db = TRUE,
      ...
    )

### Arguments

`object` | `methylRaw`, `methylRawDB`, `methylRawList`, `methylRawListDB`, `methylBase` or `methylBaseDB` object containing base pair resolution methylation information
`win.size` | an integer for the size of the tiling windows
`step.size` | an integer for the step size of tiling windows
`cov.bases` | minimum number of bases to be covered in a given window
`mc.cores` | number of cores to use when processing `methylDB` objects, default: 1, but always 1 for Windows)
`save.db` | A Logical to decide whether the resulting object should be saved as flat file database or not, default: explained in Details sections
`...` | optional Arguments used when save.db is TRUE `suffix` A character string to append to the name of the output flat file database, only used if save.db is true, default actions: append “_tiled” to current filename if database already exists or generate new file with filename “sampleID_tiled” or “methylBase_tiled” dependent on input object `dbdir` The directory where flat file database(s) should be stored, defaults to getwd(), working directory for newly stored databases and to same directory for already existing database

### Value

`methylRaw`,`methylBase` or `methylRawList` object

### Details

The parameter `chunk.size` is only used when working with `methylRawDB`, `methylBaseDB` 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`.

The parameter `save.db` is per default TRUE for methylDB objects as `methylRawDB`, `methylBaseDB` or `methylRawListDB`, while being per default FALSE for `methylRaw`, `methylBase` or `methylRawList`. If you wish to save the result of an in-memory-calculation as flat file database or if the size of the database allows the calculation in-memory, then you might want to change the value of this parameter.

### Examples

    data(methylKit)

    tiled.methylRaw=tileMethylCounts(object=methylRawList.obj,win.size=1000,
                                     step.size=1000,cov.bases=0)

[Package methylKit version 1.16.1 Index]