quartetStarTestInd: Multiple independent hypothesis tests for gene quartet counts...

In MSCquartets: Analyzing Gene Tree Quartets under the Multi-Species Coalescent

Multiple independent hypothesis tests for gene quartet counts fitting a species quartet star tree under the MSC

Description

Perform hypothesis tests for a species quartet star tree vs. any alternative for all quartet counts in an input table, as if the quartets are independent.

Usage

quartetStarTestInd(rqt)

Arguments

rqt	Table of resolved quartet counts, as produced by quartetTableResolved, or quartetTreeTestInd

Details

This function assumes all quartets are resolved. The test performed is described in quartetStarTest.

Value

the same table as the input rqt with column "p_star" appended, containing p-values for judging fit to MSC on a star tree

See Also

quartetStarTest, quartetTreeTest, quartetTreeTestInd, quartetTableResolved, quartetTestPlot

Examples

gtrees=read.tree(file=system.file("extdata","dataGeneTreeSample",package="MSCquartets"))
tnames=taxonNames(gtrees)
QT=quartetTable(gtrees,tnames[1:6])
RQT=quartetTableResolved(QT)
pTable=quartetStarTestInd(RQT)
quartetTablePrint(pTable[1:6,])

MSCquartets documentation built on April 4, 2025, 5:14 a.m.