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(
  db = RaMP(),
  fishers_df,
  perc_analyte_overlap = 0.5,
  min_pathway_tocluster = 2,
  perc_pathway_overlap = 0.5
)

Arguments

fishers_df	The full result object generated by runCombinedFisherTest
perc_analyte_overlap	Minimum overlap for pathways to be considered similar (Default = 0.5)
min_pathway_tocluster	Minimum number of 'similar' pathways required to start a cluster (medoid) (Default = 3)
perc_pathway_overlap	Minimum overlap for clusters to merge (Default = 0.5)

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: 
pkg.globals <- setConnectionToRaMP(
  dbname = "ramp2", username = "root",
  conpass = "", host = "localhost"
)
pathwaydf <- getPathwayFromAnalyte(c(
  "ensembl:ENSG00000135679", "hmdb:HMDB0000064",
  "hmdb:HMDB0000148", "ensembl:ENSG00000141510"
))
fisher.results <- runCombinedFisherTest(pathwaydf = pathwaydf)
clustered.fisher.results <- findCluster(fisher.results)

## End(Not run)

ncats/RaMP-DB documentation built on June 1, 2024, 9:34 p.m.