Question

DEXSeqHTML and biomart object

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ZheFrench ▴ 60

@zhefrench-11689

Last seen 3 months ago

France

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

DEXSeq • 1.5k views

ADD COMMENT • link updated 7.0 years ago by Alejandro Reyes ★ 1.9k • written 7.1 years ago by ZheFrench ▴ 60

score 1 · Accepted Answer · 2017-12-06

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Alejandro Reyes ★ 1.9k

@alejandro-reyes-5124

Last seen 5 months ago

Novartis Institutes for BioMedical Rese…

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 COMMENT • link 7.0 years ago Alejandro Reyes ★ 1.9k

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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 REPLY • link 6.7 years ago Matthew Thornton ▴ 380

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

Another minimal example:

library(DEXSeq)
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 REPLY • link 6.7 years ago Alejandro Reyes ★ 1.9k