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(
  cl1,
  cl2,
  na.string = "na",
  cl1.srt,
  cl2.srt,
  alternative = c("greater")
)

Arguments

cl1	clustering 1; a vector of cluster associations or an object of class "clustering" by segmenTier's clusterTimeseries
cl2	clustering 2; see argument cl1
na.string	replace NA or empty strings by ‘<na.string>’
cl1.srt	optional cluster sorting of clustering 1
cl2.srt	optional cluster sorting of clustering 2
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

raim/segmenTools documentation built on March 20, 2024, 6:23 a.m.