edge (version 2.4.2)

getCounts: Extract Specified Component of a DGEList Object

Description

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.

Usage

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

Arguments

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)

Value

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

See Also

DGEList-class

Examples

# 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)