sumTechReps: Sum Over Replicate Samples

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

Description

Condense the columns of a matrix or DGEList object so that counts are summed over technical replicate samples.

Usage

## Default S3 method:
sumTechReps(x, ID=colnames(x), ...)
## S3 method for class 'DGEList'
sumTechReps(x, ID=colnames(x), ...)
## S3 method for class 'SummarizedExperiment'
sumTechReps(x, ID, ...)

Arguments

x	a numeric matrix or DGEList object.
ID	sample identifier.
...	other arguments are not currently used.

Details

A new matrix or DGEList object is computed in which the counts for technical replicate samples are replaced by their sums.

Value

A data object of the same class as x with a column for each unique value of ID. For a SummarizedExperiment object, it is converted into a DGEList object. Columns are in the same order as the ID values first occur in the ID vector.

Author(s)

Gordon Smyth and Yifang Hu

See Also

rowsum.

Examples

x <- matrix(rpois(8*3,lambda=5),8,3)
colnames(x) <- c("a","a","b")
sumTechReps(x)

Example output

Loading required package: limma
      a b
[1,]  8 5
[2,] 12 4
[3,] 12 3
[4,] 12 0
[5,]  9 2
[6,]  9 8
[7,]  5 6
[8,] 13 5

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