reorganize {methylKit} | R Documentation

## Reorganize methylKit objects by creating new objects from subset of samples

### Description

The function creates a new `methylRawList`, `methylRawListDB`, `methylBase` or `methylBaseDB` object by selecting a subset of samples from the input object, which is a `methylRawList` or `methylBase` object. You can use the function to partition a large methylRawList or methylBase object to smaller object based on sample ids or when you want to reorder samples and/or give a new treatmet vector.

### Usage

    reorganize(methylObj, sample.ids, treatment, chunk.size = 1e+06,
      save.db = FALSE, ...)

    ## S4 method for signature 'methylBase'
    reorganize(methylObj, sample.ids, treatment,
      chunk.size = 1e+06, save.db = FALSE, ...)

    ## S4 method for signature 'methylRawList'
    reorganize(methylObj, sample.ids, treatment,
      chunk.size = 1e+06, save.db = FALSE, ...)

    ## S4 method for signature 'methylRawListDB'
    reorganize(methylObj, sample.ids, treatment,
      chunk.size = 1e+06, save.db = TRUE, ...)

    ## S4 method for signature 'methylBaseDB'
    reorganize(methylObj, sample.ids, treatment,
      chunk.size = 1e+06, save.db = TRUE, ...)

### Arguments

`methylObj` | a `methylRawList`, `methylRawListDB`, `methylBase` or `methylBaseDB` object
`sample.ids` | a vector for sample.ids to be subset. Order is important and the order should be similar to treatment. sample.ids should be a subset or reordered version of sample ids in the input object.
`treatment` | treatment vector, should be same length as sample.ids vector
`chunk.size` | Number of rows to be taken as a chunk for processing the `methylBaseDB` or `methylRawListDB` objects, default: 1e6
`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: For “methylBase”: The default suffix is a 13-character random string appended to the fixed prefix “methylBase”, e.g. “methylBase_16d3047c1a254.txt.bgz”. For “methylRawList”: ignored. `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 "tabix"

### Value

returns a `methylRawList`, `methylRawListDB`, `methylBase` or `methylBaseDB` object depending on the input object

### Details

The parameter `chunk.size` is only used when working with `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 `methylBaseDB` and `methylRawListDB`, while being per default FALSE for `methylBase` and `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

    # this is a list of example files, ships with the package
    file.list=list( system.file("extdata", "test1.myCpG.txt", package = "methylKit"),
                   system.file("extdata", "test2.myCpG.txt", package = "methylKit"),
                   system.file("extdata", "control1.myCpG.txt", package = "methylKit"),
                   system.file("extdata", "control2.myCpG.txt", package = "methylKit") )

    # read the files to a methylRawList object: myobj
    myobj=methRead( file.list,
              sample.id=list("test1","test2","ctrl1","ctrl2"),
              assembly="hg18",pipeline="amp",treatment=c(1,1,0,0))
    meth=unite(myobj,destrand=TRUE)

    # get samples named "test1" and "ctrl2" from myobj and create a new methylRawList object
    myobj2=reorganize(myobj,sample.ids=c("test1","ctrl2"),treatment=c(1,0) )

    # # get samples named "test1" and "ctrl2" from meth and create a new methylBase object
    meth2 =reorganize(meth,sample.ids=c("test1","ctrl2"),treatment=c(1,0) )

[Package methylKit version 1.12.0 Index]