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calcNormOffsetsforChIP <- function(input,response,dispersion=0.01,niter=6,loss="p",plot=FALSE,verbose=FALSE,...)
# Normalize ChIP-Seq counts to input and form offset matrix
# Gordon Smyth
# 14 Dec 2011. Last modified 14 May 2012.
{
input <- as.matrix(input)
y <- as.matrix(response)
if(nrow(input) != nrow(y)) stop("nrows of input and response disagree")
if(ncol(input)==1 && ncol(y)>1) input <- matrix(input,nrow(input),ncol(response))
if(ncol(input) != ncol(y)) stop("ncols of input and response disagree")
offset <- y
for (j in 1:ncol(y)) {
out <- normalizeChIPtoInput(input[,j],y[,j],dispersion=dispersion,niter=niter,loss=loss,plot=plot,verbose=verbose,main=colnames(y)[j],...)
offset[,j] <- log(out$scaling.factor * input[,j])
}
if(is(response,"DGEList")) {
response$offset <- offset
return(response)
} else {
return(offset)
}
}
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