subsetting {edgeR} | R Documentation |
Extract a subset of a DGEList
, DGEGLM
, DGEExact
or DGELRT
object.
## S3 method for class 'DGEList' object[i, j, ...] ## S3 method for class 'DGEGLM' object[i, j, ...] ## S3 method for class 'DGEExact' object[i, j, ...] ## S3 method for class 'DGELRT' object[i, j, ...]
object |
object of class |
i,j |
elements to extract. |
... |
not used |
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.
An object of class DGEList
, DGEGLM
, DGEExact
or DGELRT
as appropriate, holding data from the specified subset of tags/genes and libraries.
Davis McCarthy, Gordon Smyth
Extract
in the base package.
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