subsetting {limma} | R Documentation

## Subset RGList, MAList, EListRaw, EList, MArrayLM or TestResults Objects

### Description

Return an `RGList`, `MAList`, `EListRaw`, `EList`, `MArrayLM` or `TestResults` object with only selected rows and columns of the original object.

### Usage

    ## S3 method for class 'EList'
    object[i, j, ...]
    subsetListOfArrays(object, i, j, IJ, IX, I, JX)

### Arguments

`object` | object of class `RGList`, `MAList`, `EListRaw`, `EList`, `MArrayLM` or `TestResults`.
`i,j` | elements to extract. `i` subsets the probes or spots while `j` subsets the arrays.
`IJ` | character vector giving names of components that should be subsetted by `i` and `j`.
`IX` | character vector giving names of 2-dimensional components that should be subsetted by `i` only.
`I` | character vector giving names of vector components that should be subsetted by `i`.
`JX` | character vector giving names of 2-dimensional components whose row dimension corresponds to `j`.
`...` | other arguments are not currently used.

### Details

All these objects can be subsetted as if they were matrices. `i,j` may take any values acceptable for the matrix components of `object`. Either or both can be missing. See the Extract help entry for more details on subsetting matrices.

`object[]` will return the whole object unchanged. A single index `object[i]` will be taken to subset rows, so `object[i]` and `object[i,]` are equivalent.

`subsetListOfArrays` is used internally as a utility function by the subsetting operations. It is not intended to be called directly by users. Values must be supplied for all arguments other than `i` and `j`.

### Value

An object the same as `object` but containing data from the specified subset of rows and columns only.

Note the output object is of the same class as `object` will have two dimensions attached even if `i` or `j` select a single row or column, i.e., subsetting for these objects does not drop dimensions. Subsetting is exactly analogous to subsetting of matrices in R with `drop=FALSE`.

### Author(s)

Gordon Smyth

### See Also

`Extract` in the base package.

02.Classes for a summary of the different data classes.

### Examples

    M <- A <- matrix(11:14,4,2)
    rownames(M) <- rownames(A) <- c("a","b","c","d")
    colnames(M) <- colnames(A) <- c("A","B")
    MA <- new("MAList",list(M=M,A=A))
    MA[1:2,]
    MA[c("a","b"),]
    MA[1:2,2]
    MA[,2]

[Package limma version 3.44.3 Index]