extract {methylKit} | R Documentation

## extract parts of methylRaw,methylRawDB,methylBase,methylBaseDB and methylDiff data

### Description

The function extracts part of the data and returns a new object.

### Usage

    ## S4 method for signature 'methylRaw,ANY,ANY,ANY'
    x[i, j]

    ## S4 method for signature 'methylBase,ANY,ANY,ANY'
    x[i, j]

    ## S4 method for signature 'methylDiff,ANY,ANY,ANY'
    x[i, j]

    ## S4 method for signature 'methylRawDB,ANY,ANY,ANY'
    x[i, j]

    ## S4 method for signature 'methylBaseDB,ANY,ANY,ANY'
    x[i, j]

    ## S4 method for signature 'methylDiffDB,ANY,ANY,ANY'
    x[i, j]

### 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.
`j` | This argument can not be used for the extraction of columns. As unintentional extraction of the columns will cause an error in the downstream analysis. Using this argument will cause an error. Use `getData` to access the data part of the objects.

### Examples

    data(methylKit)

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

    # selects first hundred rows, returns a methylBase object
    subset2=methylBase.obj[1:100,]

    # selects first hundred rows, returns a methylDiff object
    subset3=methylDiff.obj[1:100,]

    # This will get chromomsomes, will return a factor
    # That means the resulting object will ceases to be a methylKit object
    chrs=methylDiff.obj[[2]]

[Package methylKit version 1.10.0 Index]