[BioC] getting RPKM or TPM values

Steve Lianoglou lianoglou.steve at gene.com
Thu Oct 31 19:32:29 CET 2013

Hi Nick

FIrst, please use "reply-all" when replying to emails from the list so we can keep the thread on list and other can help.


On Oct 31, 2013, at 11:22 AM, "Nikolay N." <nikolay12 at gmail.com> wrote:

> Thanks, Steve.
> I had a look at it but I am concerned about the gene.length parameter. It expects a vector of length nrow(x) giving gene length in bases. Is this already part of the DGEList object or I have to compile that list separately?

This is something you will have to provide yourself, actually.

You can look at the source code for the function by just typing its name (w/o `()` in your REPL):

R> rpkm
[source code dump here]

When you do that, you'll see that gene.length is "any old" (numeric) vector. You'll have to ensure that the i'th element in that vector matches up to the i'th row of your DGEList prior to calling that function.


Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology

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