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addPriorCount <- function(y, lib.size=NULL, offset=NULL, prior.count=1)
# Add library size-adjusted prior counts to values of 'y'.
# Also add twice the adjusted prior to the library sizes,
# which are provided as log-transformed values in 'offset'.
#
# written by Aaron Lun
# created 26 September 2016
# last modified 4 Nov 2018
{
# Check y
y <- as.matrix(y)
if (!is.numeric(y)) stop('count matrix must be numeric')
# Check prior.count
prior.count <- .compressPrior(y, prior.count)
# Check lib.size and offset.
# If offsets are provided, they must have a similar average to log(lib.size)
# for the results to be meaningful as logCPM values
offset <- .compressOffsets(y, lib.size=lib.size, offset=offset)
# Adding the prior count.
out <- .Call(.cxx_add_prior_count, y, offset, prior.count)
names(out) <- c("y", "offset")
dimnames(out$y) <- dimnames(y)
out$offset <- makeCompressedMatrix(out$offset, dim(y), byrow=TRUE)
return(out)
}
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