subsetting: Subset DGEList, DGEGLM, DGEExact and DGELRT Objects

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

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

Example output

Loading required package: limma
An object of class "DGEList"
$counts
  A1 A2 B1 B2
a 66  1 11  0
b  4  1 43  8

$samples
   group lib.size norm.factors
A1     A      138            1
A2     A       11            1
B1     B       64            1
B2     B        9            1

An object of class "DGEList"
$counts
  A2
a  1
b  1

$samples
   group lib.size norm.factors
A2     A       11            1

An object of class "DGEList"
$counts
  A2
a  1
b  1
c  9
d  0

$samples
   group lib.size norm.factors
A2     A       11            1

An object of class "DGEExact"
$table
      logFC   logCPM      PValue
a -1.406454 17.94948 0.150924386
b  4.214324 18.60396 0.002036875

$comparison
[1] "A" "B"

edgeR documentation built on Jan. 16, 2021, 2:03 a.m.