protViz / prora

running ora or gsea on lists of proteinidentifiers

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Open lisajohanna opened 4 years ago

lisajohanna commented 4 years ago

Get sigora working for various ID types.

MSIGDB (lisa)

using Uniprot https://github.com/protViz/fgcz.gsea.ora/blob/master/R/make_ids_uniprot.R
use MSIGDB r package to map ENTREZ ids to genesets from MSIG and get it running with sigora.
dplry::inner_join(uniprot_entrez, msig_DB, by ="entrez_ID")

wolski commented 4 years ago

Is sigora::idmap used when ID's in query list map those in gpsRepo?

What is the level argument in the sigora function and how does work? How are hierarchical gpsRepo's created?