Hello, I think have problem with writing this command, could you please explain where went wrong exactly with collapseReplicates command?

thanks in advance

gr <- factor(c(rep("Dnmt2_ND", 2), rep("Dnmt2_NF", 2), rep("Dnmt2_HD", 2), rep("Dnmt2_HF", 2)))

colData <- data.frame(group=gr, type="paired-end")

cds <- DESeqDataSetFromMatrix(cn3, colData, design= ~group)

cds <- DESeq(cds)

cnt <- log2(1+counts(cds, normalized=T))

cntColl <- collapseReplicates(cnt, gr, renameCols = TRUE)

Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘assay’ for signature ‘"matrix", "missing"’

The "unable to find method" error can be interpreted as R saying "you can't run that function on this type of data". 

The next step should be to look up the function, ?collapseReplicates, and see what it's first argument should be. You can figure out what class of object you have with class():

class(dds)
class(cnt)