Subset DGEList, DGEGLM, DGEExact and DGELRT Objects
Extract a subset of a DGEList, DGEGLM, DGEExact or DGELRT object.
## 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]
object |
object of class |
i,j |
elements to extract. |
keep.lib.sizes |
logical, if |
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 the same class as object holding data from the specified subset of rows and columns.
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 objectsPlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.