richCluster: kappa cluster analysis

In hurlab/RichR: Function Enrichment analysis and Network construction

kappa cluster analysis

Description

kappa cluster analysis

Usage

richCluster(
  x,
  gene = NULL,
  useTerm = FALSE,
  cutoff = 0.5,
  overlap = 0.5,
  minSize = 5,
  escore = 3
)

Arguments

x	richResult object or dataframe
gene	(Optional).a vector of gene list
useTerm	to use the term or not (TRUE/FALSE)
cutoff	kappa score threshold for significant dispersion results
overlap	cutoff value of the overlap between two Terms
minSize	minimal number of terms in the cluster
escore	kappa enrichment score cutoff value (default: 3)

Author(s)

Kai Guo

Examples

## Not run: 
  hsago<-buildAnnot(species="human",keytype="SYMBOL",anntype = "GO")
  gene<-ample(unique(hsago$GeneID),1000)
  res<-richGO(gene,godata = hsago,ontology ="BP")
  resc<-richCluster(res)

## End(Not run)

hurlab/RichR documentation built on Feb. 5, 2024, 8:07 p.m.