Question: DEXSeqHTML and biomart object
gravatar for ZheFrench
11 months ago by
ZheFrench10 wrote:

Could you provide a more detailed example of code to use biomart object and extra columns to add for example GeneSymbol in the output of DEXSeqHTML  ?

Not clear to me how you use mart  and attributes parameters in DEXSeqHTML


ADD COMMENTlink modified 11 months ago by Alejandro Reyes1.6k • written 11 months ago by ZheFrench10
gravatar for Alejandro Reyes
11 months ago by
Alejandro Reyes1.6k
Dana-Farber Cancer Institute, Boston, USA
Alejandro Reyes1.6k wrote:

Hi! The easiest way to do that would be something along these lines:



data("pasillaDEXSeqDataSet", package="pasilla")
dxr <- DEXSeq( dxd )

mart <- useMart( biomart="ensembl", dataset="dmelanogaster_gene_ensembl" )
extraCols <- getBM(attributes=c("ensembl_gene_id", "ensembl_peptide_id"), filter="ensembl_gene_id",
                   mart=mart, values=geneIDs(dxd) )
extraCols <- extraCols[!duplicated(extraCols$ensembl_gene_id),]
rownames(extraCols) <- extraCols$ensembl_gene_id
DEXSeqHTML( dxr, extraCols=extraCols )


ADD COMMENTlink written 11 months ago by Alejandro Reyes1.6k

Ok so this looks like the answer to my question, sorry I didn't see it first.  I am confused, how do you know for sure that the 'ensembl_gene_id' lines up with the 'ensembl_gene_id' in dxr?  I guess because you pull from it  initially with values=geneIDs(dxd)?  Thanks!!

ADD REPLYlink written 7 months ago by Matthew Thornton290

Names are matched based on the rownames of extraCols. Thus, the rownames of extraCols should match what is stored in geneIDs(). 

Another minimal example:

data(pasillaDEXSeqDataSet, package="pasilla")
dxr <- DEXSeq( dxd )
extraCols <- data.frame( ids=unique(geneIDs(dxd)), mygeneIDs=sprintf("gene%0.3d", seq_along(unique(geneIDs(dxd)))))
rownames(extraCols) <- extraCols$ids
DEXSeqHTML( object=dxr, extraCols=extraCols )
ADD REPLYlink modified 7 months ago • written 7 months ago by Alejandro Reyes1.6k
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