subsetting {edgeR} | R Documentation

## Subset DGEList, DGEGLM, DGEExact and DGELRT Objects

### Description

Extract a subset of a `DGEList`, `DGEGLM`, `DGEExact` or `DGELRT` object.

### Usage

    ## S3 method for class 'DGEList'
    object[i, j, keep.lib.sizes=TRUE]
    ## S3 method for class 'DGEGLM'
    object[i, j]
    ## S3 method for class 'DGEExact'
    object[i, j]
    ## S3 method for class 'DGELRT'
    object[i, j]
    ## S3 method for class 'TopTags'
    object[i, j]

### Arguments

`object` | object of class `DGEList`, `DGEGLM`, `DGEExact` or `DGELRT`. For `subsetListOfArrays`, any list of conformal matrices and vectors.
`i,j` | elements to extract. `i` subsets the genes while `j` subsets the libraries. Note that columns of `DGEGLM`, `DGEExact` and `DGELRT` objects cannot be subsetted.
`keep.lib.sizes` | logical, if `TRUE` the lib.sizes will be kept unchanged on output, otherwise they will be recomputed as the column sums of the counts of the remaining rows.

### Details

`i,j` may take any values acceptable for the matrix components of `object` of class `DGEList`. See the Extract help entry for more details on subsetting matrices. For `DGEGLM`, `DGEExact` and `DGELRT` objects, only rows (i.e. `i`) may be subsetted.

### Value

An object of the same class as `object` holding data from the specified subset of rows and columns.

### Author(s)

Davis McCarthy, Gordon Smyth

### See Also

`Extract` in the base package.

### Examples

    d <- matrix(rnbinom(16,size=1,mu=10),4,4)
    rownames(d) <- c("a","b","c","d")
    colnames(d) <- c("A1","A2","B1","B2")
    d <- DGEList(counts=d,group=factor(c("A","A","B","B")))
    d[1:2,]
    d[1:2,2]
    d[,2]
    d <- estimateCommonDisp(d)
    results <- exactTest(d)
    results[1:2,]
    # NB: cannot subset columns for DGEExact objects

[Package edgeR version 3.20.9 Index]