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saezlab / SLAPenrich

Sample Level Analysis of Pathway Alteration Enrichments
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attempt to select less than one element in get1index #7

Open complexgenome opened 3 months ago

complexgenome commented 3 months ago

Hi there, I use following command for core components:

SLAPE.core_components(PFP=kegg_SLAPE_analysis,
                      EM=df_mutation,
                      PATH='/data1/users/sanjeev/slapenrich/kegg_database/n786_cov80_',
                      exclcovth=80,fdrth=5,
                      PATH_COLLECTION = KEGG_PATH)

I get error as:

Error in PATH_COLLECTION$HGNC_SYMBOL[[PFP$pathway_id[i]]] : attempt to select less than one element in get1index

I believe it's because no pathway survived filtering of both FDR as well as coverage.