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getOffset <- function(y)
# Extract offset vector or matrix from data object and optional arguments.
# By default, offset is constructed from the lib.size and norm.factors
# but offset supplied explicitly takes precedence
# Gordon Smyth
# 26 Jan 2011. Last modified 11 Jan 2012.
{
offset <- y$offset
lib.size <- y$samples$lib.size
norm.factors <- y$samples$norm.factors
if(!is.null(offset)) {
return(offset)
} else {
if(!is.null(norm.factors)) lib.size <- lib.size*norm.factors
return(log(lib.size))
}
}
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