Entering edit mode
2.7 years ago
shail.nair05
▴
20
Hi, I am new to clusterProfiler. Is it possible to use clusterProfiler for metatranscriptomics DEG data (deseq2)? As i read from http://yulab-smu.top/clusterProfiler-book/chapter3.html#input-data for unsupported organisms, one need to create TERM2GENE and TERM2NAME file, which according to the guide requires a organism specfic gmt file.
My sample is of mixed bacterial transcript expression (metatranscriptomics). I ran deseq2 and wanted to do functional gene enrichment analysis.
TERM2NAME is optional. TERM2GENE is a
data.frame
with first column of term ID (wpid
)and second column of corresponding mappedgene
:In the example above the term ID correspond to the wikipathway IDs but can be any annotation term (e.g. Gene Ontology ID). For metagenomic/metatranscriptomic data you can use eggNOG to annotate your transcripts with
GO
Thanks. is it possible to use kegg for metagenomic/metatranscriptomic?
Yes, you can use KEGG pathways id instead of GO. eggNOG will also annotate your transcripts with the KEGG annotation terms.
will try with kegg. Thanks :)