getCounts: Extract Specified Component of a DGEList Object
In hiraksarkar/edgeR_fork: Empirical Analysis of Digital Gene Expression Data in R

Description Usage Arguments Value Author(s) See Also Examples

getCounts(y) returns the matrix of read counts y$counts.

getOffset(y) returns offsets for the log-linear predictor account for sequencing depth and possibly other normalization factors. Specifically it returns the matrix y$offset if it is non-null, otherwise it returns the log product of lib.size and norm.factors from y$samples.

getDispersion(y) returns the most complex dispersion estimates (common, trended or genewise) found in y.

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getCounts(y) 
getOffset(y) 
getDispersion(y)

`y`	`DGEList` object containing (at least) the elements `counts` (table of raw counts), `group` (factor indicating group) and `lib.size` (numeric vector of library sizes)

getCounts returns the matrix of counts. getOffset returns a numeric matrix or vector. getDispersion returns vector of dispersion values.

Mark Robinson, Davis McCarthy, Gordon Smyth

DGEList-class

# generate raw counts from NB, create list object
y <- matrix(rnbinom(20,size=5,mu=10),5,4)
d <- DGEList(counts=y, group=c(1,1,2,2), lib.size=1001:1004)
getCounts(d)
getOffset(d)
d <- estimateCommonDisp(d)
getDispersion(d)