getMethylDiff {methylKit} | R Documentation

## get differentially methylated regions/bases based on cutoffs

### Description

The function subsets a `methylDiff` or `methylDiffDB` object in order to get differentially methylated bases/regions satisfying thresholds.

### Usage

    getMethylDiff(
      .Object,
      difference = 25,
      qvalue = 0.01,
      type = "all",
      chunk.size = 1e+06,
      save.db = FALSE,
      ...
    )

    ## S4 method for signature 'methylDiff'
    getMethylDiff(
      .Object,
      difference = 25,
      qvalue = 0.01,
      type = "all",
      chunk.size = 1e+06,
      save.db = FALSE,
      ...
    )

    ## S4 method for signature 'methylDiffDB'
    getMethylDiff(
      .Object,
      difference = 25,
      qvalue = 0.01,
      type = "all",
      chunk.size = 1e+06,
      save.db = TRUE,
      ...
    )

### Arguments

`.Object` | a `methylDiff` or `methylDiffDB` object
`difference` | cutoff for absolute value of methylation percentage change between test and control (default:25)
`qvalue` | cutoff for qvalue of differential methylation statistic (default:0.01)
`type` | one of the "hyper","hypo" or "all" strings. Specifies what type of differentially menthylated bases/regions should be returned. For retrieving Hyper-methylated regions/bases type="hyper", for hypo-methylated type="hypo" (default:"all")
`chunk.size` | Number of rows to be taken as a chunk for processing the `methylDiffDB` objects (default: 1e6)
`save.db` | A Logical to decide whether the resulting object should be saved as flat file database or not, default: see Details
`...` | 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 “_type” to current filename if database already exists or generate new file with filename “methylDiff_type” `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 `dbtype` The type of the flat file database, currently only option is "tabix" (only used for newly stored databases)

### Value

a methylDiff or methylDiffDB object containing the differential methylated locations satisfying the criteria

### Details

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

The parameter `save.db` is per default TRUE for methylDB objects as `methylDiffDB`, while being per default FALSE for `methylDiff`. 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)

    # get differentially methylated bases/regions with specific cutoffs
    all.diff=getMethylDiff(methylDiff.obj,difference=25,qvalue=0.01,type="all")

    # get hyper-methylated
    hyper=getMethylDiff(methylDiff.obj,difference=25,qvalue=0.01,type="hyper")

    # get hypo-methylated
    hypo=getMethylDiff(methylDiff.obj,difference=25,qvalue=0.01,type="hypo")

[Package methylKit version 1.20.0 Index]