findCluster: Perform fuzzy multiple linkage partitioning clustering on...

In ncats/RaMP-DB: RaMP (Relational Database of Metabolomic Pathways)

Perform fuzzy multiple linkage partitioning clustering on pathways identified by Fisher's test

Description

Perform fuzzy multiple linkage partitioning clustering on pathways identified by Fisher's test

Usage

findCluster(
  fishersDf,
  percAnalyteOverlap = 0.5,
  minPathwayToCluster = 2,
  percPathwayOverlap = 0.5,
  db = RaMP(),
  ...
)

Arguments

fishersDf	The full result object generated by runEnrichPathways
percAnalyteOverlap	Minimum overlap for pathways to be considered similar (Default = 0.5)
minPathwayToCluster	Minimum number of 'similar' pathways required to start a cluster (medoid) (Default = 3)
percPathwayOverlap	Minimum overlap for clusters to merge (Default = 0.5)
db	a RaMP database object
...	Internal Use - for handling deprecated parameter names

Value

list:[[1]] Pathway enrichment result with dataframe having a cluster assignment column added [[2]] analyte type [[3]] cluster assignment in the list form

Examples

## Not run: 
pathways.enriched <- runEnrichPathways(
analytes = c("hmdb:HMDB0000033","hmdb:HMDB0000052","hmdb:HMDB0000094",
             "hmdb:HMDB0000161","hmdb:HMDB0000168","hmdb:HMDB0000191","hmdb:HMDB0000201",
             "chemspider:10026","hmdb:HMDB0006059", "Chemspider:6405", "CAS:5657-19-2",
             "hmdb:HMDB0002511", "chemspider:20171375","CAS:133-32-4", "CAS:5746-90-7",
             "CAS:477251-67-5", "hmdb:HMDB0000695", "chebi:15934", "CAS:838-07-3",
             "hmdb:HMDBP00789", "hmdb:HMDBP00283", "hmdb:HMDBP00284", "hmdb:HMDBP00850"),
db=rampDB)

filtered.pathways.enriched <- filterEnrichResults(enrichResults=pathways.enriched,
                                                  pValType = 'holm', pValCutoff=0.05)

clusters <- findCluster(filtered.pathways.enriched, percAnalyteOverlap = 0.2,
                        percPathwayOverlap = 0.2, db=rampDB)

## End(Not run)

ncats/RaMP-DB documentation built on June 10, 2025, 10:50 a.m.