This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Annotation Columns In Dexseq Html Report

Hi All I am using DEXSeq to identify differential exon usage in my dataset that has two conditions. I was able to follow all the instructions from the vignettes/manuals for the tool and produce a nice final report. However, I wanted to display external gene ID (gene symbol) and description of the gene in the final reports as two additional columns. I saw several examples posted by various people that shows a report with these two columns. However, I didn't find any specific instructions as to how I can do that. I am a newbie with R packages & bioconductor in general and maybe asking a very basic question..but I would really appreciate any help I can get. Thanks.

splicing exon differential r
• 3,220 views • link
written by pm2013 • pm2013

1 answer

After a little bit of tinkering around I was able to find a solution. Here's what I used to get my desired output. Few more steps are required prior to this tho (e.g creating object called mart etc.) Here's a copy/paste: DEXSeqHTML(ecs,geneIDs=NULL,fitExpToVar="condition",FDR=0.1, color=c("#FF000080","#0000FF80"),mart=ensembl,filter="ensembl_gene_id",attributes=c("external_gene_id","description"),nCores=18)

• 0 views • link
written by pm2013 • pm2013

Log in to answer this question.

More posts like this