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

Description Usage Arguments Value Examples

View source: R/rampFastQueryTab3.R

Description

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

Usage

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findCluster(fishers_df, perc_analyte_overlap = 0.5,
  min_pathway_tocluster = 2, perc_pathway_overlap = 0.5)

Arguments

fishers_df

The data frame generated by runFisherTest

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 dataframe with cluster assignment column added [[2]] analyte type [[3]] cluster assignment in the list form

Examples

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## Not run: 
pathwaydf<-getPathwayFromAnalyte(c("MDM2","TP53","glutamate","creatinine"),
                NameOrIds="names", conpass=conpass)
fisher.results <- runCombinedFisherTest(pathwaydf=pathwaydf,conpass=conpass)
filtered.fisher.results <- FilterFishersResults(fisher.results,p_holmadj_cutoff=0.05)
filteredclust.fisher.results <- findCluster(filtered.fisher.results)

## End(Not run)

ncats/RaMP-DB documentation built on Nov. 21, 2020, 7:41 p.m.