Question: RnBeads, enrichment analysis
0
gravatar for gaiusjaugustus
3.0 years ago by
University of Arizona
gaiusjaugustus0 wrote:

Hi, I have completed my first DMR analysis with the 450k array data using RnBeads.  The final differential analysis line of code was:

rnb.run.differential(rnb.set, report.dir)

But an enrichment analysis wasn't run.  Here are my options.

rnb.options(filtering.sex.chromosomes.removal=TRUE, identifiers.column= "Sample_ID", import.table.separator="\t", "differential.comparison.columns"=c("TumorNormal"), "columns.pairing"=c("TumorNormal"="Sample_Name"), inference.targets.sva=c("Sample_Group"), inference.sva.num.method="be")

 

I assume that I forgot to put something here, but any help would be appreciated.  I'd like to run my enrichment analysis on my differentially methylated regions (genes).

rnbeads • 501 views
ADD COMMENTlink written 3.0 years ago by gaiusjaugustus0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 192 users visited in the last hour