Hi,
I would like to get RPKM or TPM values for a rna-seq study. How can I
get
in the most straight-forward way from a DGEList object in edgeR?
Alternatively, if you are aware of another R package which makes it
easy to
get these values - please let me know.
many thanks,
Nick
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Hi Nick,
On Thu, Oct 31, 2013 at 9:17 AM, Nikolay N. <nikolay12 at="" gmail.com="">
wrote:
> Hi,
>
> I would like to get RPKM or TPM values for a rna-seq study. How can
I get
> in the most straight-forward way from a DGEList object in edgeR?
>
> Alternatively, if you are aware of another R package which makes it
easy to
> get these values - please let me know.
Read through the documentation for the edgeR::cpm function:
R> ?cpm
-steve
--
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech
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.
Now:
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.
HTH,
-steve
--
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech
Thanks!
On Thu, Oct 31, 2013 at 6:32 PM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:
> 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.
>
> Now:
>
>
> On Oct 31, 2013, at 11:22 AM, "Nikolay N." <nikolay12@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.
>
> HTH,
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
>
>
>
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