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Question: DEXSeqHTML and biomart object
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gravatar for ZheFrench
12 weeks ago by
ZheFrench10
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 10 weeks ago by Alejandro Reyes1.5k • written 12 weeks ago by ZheFrench10
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gravatar for Alejandro Reyes
10 weeks ago by
Alejandro Reyes1.5k
Dana-Farber Cancer Institute, Boston, USA
Alejandro Reyes1.5k wrote:

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

 

library(DEXSeq)
library(biomaRt)

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 10 weeks ago by Alejandro Reyes1.5k
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