[BioC] DexSeq extracols option

[Alejandro Reyes]

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
>