Question: Annotation of DEXSeqHTML with biomaRt
0
gravatar for Matthew Thornton
20 months ago by
USA, Los Angeles, USC
Matthew Thornton330 wrote:

Hello!  I am trying to annotate the output of DEXSeqHTML for ease of my collaborators.  I am using the code but not getting any annotation. Does anyone else have this problem?

DEXSeqHTML(dxr1, genes=NULL, path="DEXSeqReport", file="testForDEU.html", fitExpToVar="condition", FDR=0.1, color=NULL, color.samples=NULL, mart="ensembl", filter="ensembl_gene_id_version", attributes=c("ensembl_gene_id","external_gene_name","description"), extraCols=NULL)

I set up the biomaRt "ensembl" with the following

placeholder <- listMarts(mart = NULL, host="http://uswest.ensembl.org", path="/biomart/martservice", port=80, includeHosts>  FALSE, archive = FALSE, ssl.verifypeer = TRUE,ensemblRedirect = TRUE, verbose = FALSE)

ensembl = useDataset("hsapiens_gene_ensembl", mart=placeholder)

> ensembl
Object of class 'Mart':
  Using the ENSEMBL_MART_ENSEMBL BioMart database
  Using the hsapiens_gene_ensembl dataset>

If I use getBM with the same filters and attributes and the ensembl gene id's with version, I get the output.  Any suggestions??

biomart dexseq • 341 views
ADD COMMENTlink written 20 months ago by Matthew Thornton330

Not sure what is going wrong. Have you tried to include these names by doing the biomart call outside of DEXSeqHTML and then passing the data.frame (where the rownames are the `geneIDs()`) to the extraCols parameter?

ADD REPLYlink modified 20 months ago • written 20 months ago by Alejandro Reyes1.7k

I will try this. Can a vector be used with the attributes switch with DEXSeqHTML? Thank you!

ADD REPLYlink written 20 months ago by Matthew Thornton330

Could you post as an answer how you would add annotations using DEXSeqHTML?  I would be nice to have more, info, like the descriptions, but I would settle for just the external_gene_names. Could it be that there is not enough room in HTML table?

ADD REPLYlink written 20 months ago by Matthew Thornton330

I don't know if it's just a copy/paste error, but the code you include for setting up biomaRt has a couple of problems.  First includeHosts> FALSE should probably be includeHosts = FALSE.  Second, the output from listMarts() can't be passed to useDataset(), you want  useMart() instead.  This should set it up correctly:

placeholder <- useMart(biomart = 'ensembl', 
                       host="http://uswest.ensembl.org")
ensembl <- useDataset("hsapiens_gene_ensembl", mart = placeholder)

 

ADD REPLYlink written 20 months ago by Mike Smith4.0k
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