clusterCluster: calculates overlaps between two clusterings

In raim/segmenTools: Tools for Functional Genome Exploration

calculates overlaps between two clusterings

Description

Calculates mutual overlaps between two clusterings of the same data set using hypergeometric distribution statistics for significantly enriched or deprived mutual overlaps. The resulting tables can be plotted with plotOverlaps and sorted along one axis by signficance with plotOverlaps. TODO: specify wich cl will be rows/columns and to which percent refers to

Usage

clusterCluster(
  query,
  target,
  q.srt,
  t.srt,
  na.string = "na",
  alternative = c("greater"),
  cl1,
  cl2,
  cl1.srt,
  cl2.srt
)

Arguments

query	clustering 1; a vector of cluster associations or an object of class "clustering" by segmenTier's clusterTimeseries
target	clustering 2; see argument query
q.srt	optional cluster sorting of clustering 1
t.srt	optional cluster sorting of clustering 2
na.string	replace NA or empty strings by ‘<na.string>’
alternative	a character string specifying the alternative hypothesis, must be one of ‘"greater"’ to calculate enrichment (default), ‘"less"’ to calculate deprivation, or ‘"two.sided"’ to report the more more signficant p-value of both
cl1	obsolete: use query
cl2	obsolete: use target
cl1.srt	obsolete: use q.srt
cl2.srt	obsolte: use t.srt

raim/segmenTools documentation built on July 5, 2025, 4:34 a.m.