allHclustThreshold: Iterate 'hclustThreshold' along the specified GO ontologies...

In pablof1988/goSorensen: Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

Iterate hclustThreshold along the specified GO ontologies and GO levels

Description

Iterate hclustThreshold along the specified GO ontologies and GO levels

Usage

allHclustThreshold(x, ontos, GOLevels, trace = TRUE, ...)

Arguments

x	an object of class "distList".
ontos	"character", GO ontologies to iterate. Defaults to the ontologies in 'x'.
GOLevels	"integer", GO levels to iterate inside each one of these GO ontologies.
trace	Logical. If TRUE (default), the process is traced along the specified GO ontologies and levels.
...	extra parameters for function hclustThreshold.

Value

An object of class "equivClustSorensenList" descending from "iterEquivClust" which itself descends from class "list". It is a list with as many components as GO ontologies have been specified. Each of these elements is itself a list with as many components as GO levels have been specified. Finally, the elements of these lists are objects of class "equivClustSorensen", descending from "equivClust" which itself descends from "hclust".

Examples

# Object \code{allTabs} of class "allTableList" contains all the pairwise contingency tables of
# joint enrichment for the gene lists in \code{allOncoGeneLists}, obtained along all three GO
# ontologies and along GO levels 3 to 10:
data(allContTabs)
# Compute the Sorensen-Dice equivalence threshold dissimilarity (only for the MF and CC
# ontologies and from levels 4 to 6):
dists <- allSorenThreshold(allContTabs, ontos = c("MF", "CC"), GOLevels = seq.int(4,6))
hclusts <- allHclustThreshold(dists)
hclusts$MF$`level 6`
plot(hclusts$MF$`level 6`)

pablof1988/goSorensen documentation built on Dec. 15, 2024, 12:01 p.m.