select {methylKit} | R Documentation

## selects rows from of methylKit objects

### Description

The function returns a subset of data contained in the `methylKit` objects.

### Usage

    select(x,i)

    ## S4 method for signature 'methylBase'
    select(x, i)

    ## S4 method for signature 'methylRaw'
    select(x, i)

    ## S4 method for signature 'methylDiff'
    select(x, i)

    ## S4 method for signature 'methylRawDB'
    select(x, i)

    ## S4 method for signature 'methylBaseDB'
    select(x, i)

    ## S4 method for signature 'methylDiffDB'
    select(x, i)

### Arguments

`x` | an `methylBase`,`methylBaseDB`, `methylRaw`,`methylRawDB` or `methylDiff` object
`i` | a numeric or logical vector. This vector corresponds to bases or regions contained in `methylKit` objects.The vector is used to subset the data.

### Value

a `methylBase`,`methylRaw` or `methylDiff` object depending on the input object.

### Examples

    data(methylKit)

    methylRawDB.obj=methRead( system.file("extdata","test1.txt.bgz",package="methylKit"),
                              sample.id="test1", assembly="hg18",
                              dbtype = "tabix",dbdir = "methylDB")

    methylBaseDB.obj=unite(methylRawList.obj,save.db=TRUE,dbdir="methylDB")

     # selects first hundred rows, returns a methylRaw object
    subset1=select(methylRawList.obj[[1]],1:100)
    subset1=select(methylRawDB.obj,1:100)

    # selects first hundred rows, returns a methylBase object
    subset2=select(methylBase.obj,1:100)
    subset2=select(methylBaseDB.obj,1:100)

    # selects first hundred rows, returns a methylDiff object
    subset3=select(methylDiff.obj,1:100)

    # remove Database again
    rm(methylBaseDB.obj)
    rm(methylRawDB.obj)
    unlink("methylDB",recursive=TRUE)

[Package methylKit version 1.16.1 Index]