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Question: Add avgTxLength to DESeqDataSet
0
gravatar for rhart
4 months ago by
rhart0
rhart0 wrote:

I'd like to manually add a vector of transcript sizes to my DDS object.  I tried setting:

dds@assays$data$avgTxLength=data.frame(row.names=txOrder,"avgTxLength"=tlen[txOrder,])

Where txOrder is the row names from the dds data and tlen is the (out of order) transcript list for those row names.  The error I get when I try using fpkm() is "invalid 'dimnames' given for data frame".

How do I add this vector so I can output fpkm?

 

ADD COMMENTlink modified 4 months ago • written 4 months ago by rhart0
0
gravatar for Steve Lianoglou
4 months ago by
Genentech
Steve Lianoglou12k wrote:

Your DDS is a subclass of a summarizedexperiment. rowData(DDS) Should return you a DataFrame of gene info. So, you should be able to do something like rowData(DDS)$txlength <- xxx

Where xxx is a properly ordered vector of gene lengths

ADD COMMENTlink written 4 months ago by Steve Lianoglou12k
0
gravatar for Michael Love
4 months ago by
Michael Love15k
United States
Michael Love15k wrote:

hi,

You say vector, which sounds like you just have a single number per gene. Is that correct? In that case, if you take a look at ?fpkm, the thing to do is just:

mcols(dds)$basepairs <- x

Where x is your vector of gene lengths, lined up with rows of dds.

ADD COMMENTlink written 4 months ago by Michael Love15k

Nope, neither worked. 

I'm working at the transcript level and I have the length for each transcript (calculated with a simple script from the gtf).  So tlen is a data frame with transcript_id's as row names and one column of data labeled "Len".  txOrder is a character array with the transcript_id values used in my dds object (after filtering) in the correct order. 

Replacing "xxx" or "x" in the above examples with tlen[txOrder,] (which produces a numeric vector) still gives the "dimnames" error when I try fpkm().

 

ADD REPLYlink written 4 months ago by rhart0

Can you make a small reproducible example, so I can take a look? Ideally with just simulated data, e.g. makeExampleDESeqDataSet.

ADD REPLYlink written 4 months ago by Michael Love15k

In creating a subset example object, I can now get the mcols(dds)$basepairs<-x method to work.  So now I'll go back and re-create my original dds object--perhaps I screwed it up with my other trial methods.  But thanks--this seems to have solved my problem!

 

ADD REPLYlink written 4 months ago by rhart0
0
gravatar for rhart
4 months ago by
rhart0
rhart0 wrote:

(deleted)

 

ADD COMMENTlink modified 4 months ago • written 4 months ago by rhart0
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