[BioC] DexSeq extracols option

[Ioannis Vlachos]

Hello Alejandro and thanks for the prompt response,

I am using DEXSeq 1.6, so that was not the problem.

The second part of your advice was the solution to my torment.

I will elaborate further, just in case anyone faces a similar situation.

I was using all the geneIDs present in my ecs object. 

However, the HTML output used only the ones with significant exons (396, as
you pointed out).

So, I took all the genes from ecs, removed those with padjust less than what
I've selected for the HTML formation, kept unique geneIDs and then
downloaded the relevant info from biomaRt.

I used also as rownames the geneIDs just to play safe but I'm not sure if it
was necessary.

The derived data.frame was my input to extraCols.

It worked very nice and it embedded the extra info on the index page of the
html. Quite handy.

Thank you again for your help,

Best regards,

Ioannis



-----Original Message-----
From: Alejandro Reyes [mailto:alejandro.reyes at embl.de] 
Sent: Monday, July 29, 2013 10:42 AM
To: Ioannis Vlachos
Cc: bioconductor at r-project.org
Subject: Re: [BioC] DexSeq extracols option

Dear Ioannis,

Thanks for your message, it is usually nice and easier to track the problem
if you add the output of your sessionInfo and reproducible code, but I am
guessing that you are using a old version of DEXSeq.

The table that the HTML reporter produces a table with information for each
gene, not for each exon.  I would be almost sure that the 396 are the number
of genes that have significant exons.  As the documentation indicates, the
parameter extraCols accepts a data frame in which the rownames are genes of
your ExonCountSet object.

Let me know if this is the problem,

Best regards,
Alejandro


> Hello,
>
> A (hopefully) simple question.
>
> As I saw in ??DEXSeqHTML, there is an option to add attributes in the 
> HTML results (extracols).
>
> I downloaded from biomaRt a set aof attributes to test this (gene 
> name, biotype and description), and created a data frame having as a 
> first column the exons of my ecs  (retaining exon order), geneID and the
new attributes.
>
> The first two columns were taken by accessing fData from the ecs.
>
>   The resulting data frame naturally had an equal number of rows with 
> the exons present in my ecs object (355320).
>
> I tried to set the extracols option in a different number of ways 
> (putting as row.names the geneID or exonID, having only one column 
> etc), but I always got this error:
>
> Error in data.frame(..., check.names = FALSE) :
>    arguments imply differing number of rows: 355320, 396
>
> Where 355320 is the correct number of rows of both ecs exons and of my 
> extra attributes data.frame. (I haven't figured out what has 396 rows
yet).
>
> I checked the online reference manual and there is no mention of the 
> extracols option. I also checked the code of  the relevant function 
> and I don't see it get used somewhere.
>
> Any ideas?
>
> Is there another way to add gene or exon attributes in the HTML?
>
> Thank you all,
>
> Best regards,
>
> Ioannis
>