subsetting: Subset DGEList, DGEGLM, DGEExact and DGELRT Objects

In OliverVoogd/edgeR: Empirical Analysis of Digital Gene Expression Data in R

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

OliverVoogd/edgeR documentation built on July 28, 2022, 10:13 p.m.