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

Description Usage Arguments Details Value See Also Examples

View source: R/StarQuartetHypTest.R

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

1

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

1
2
3
4
5
6
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 Jan. 8, 2021, 2:10 a.m.