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

View source: R/ReturnPathwaysEnrich_InputAnalytes.R

findClusterR Documentation

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(
  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 May 6, 2022, 1:35 a.m.