resolveLevel1: Resolve Tree of Blobs to Level-1 network

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

Resolve Tree of Blobs to Level-1 network

Description

Given a Tree of Blobs and qcCF information, resolve all multifurcations to cycles. Resolution is performed by finding a least-squares best-fit of an empirical distance to an expected distance related to the cycle, as described in \insertCiteABRW24;textualMSCquartets.

Usage

resolveLevel1(
  ToB,
  pTable,
  test = "T3",
  alpha,
  beta,
  distance = "NANUQ",
  hdegree = 10,
  plot = 2,
  delta = 10^-6,
  fullResMax = 10
)

Arguments

ToB	an unrooted tree of blobs (phylo object) as determined by TINNIK or another method
pTable	a table of qcCFs, with columns p_star and p_test
test	either "T3" or "cut", indicating test to use for determining what qcCFs indicate hybridization
alpha	test level for p_test
beta	test level value for p_star
distance	cycle resolution distance to be used ("NANUQ" or "modNANUQ")
hdegree	resolve a multifurcation of this degree or larger by a heuristic method; must be at least 5
plot	if 0, no plots; if 1, plot only possible root locations on ToB and full resolution; if 2, include plots of each individual blob resolution, if 3 include histograms of measure of fit for all hybrid/orders considered in choosing best
delta	cutoff for relative difference in squared residuals and smallest, (RSS-minRSS)/minRSS, for determining near ties as "best" fit resolutions
fullResMax	maximum number of full resolutions (all multifurcations at once) to form; if the product of the number of resolutions of individual multifurcations exceeds this, no full resolutions are produced, although combineCycleResolutions can be applied to produce them.

Details

Possible distances to use are the NANUQ distance and a modified NANUQ distance that weights quartet trees differently, but from which the cycle structure is still identifiable.

For multifucations of degree less than a designated cutoff, all possible circular orders and choices of hybrid nodes are considered in choosing the best. Above that cutoff, a heuristic method is used to obtain a small number of orders likely to be good fits, with the least-squares fitting applied only to those.

Value

a list of resolutions and squared residuals:

• [[1]] is a list of Newick resolutions of entire network, with all edge lengths 1 (NULL if one cannot be produced or fullResMax is exceeded),

• [[2]]-[[n]] are individual resolutions of each multifurcation on ToB, each given as a list as output from resolveCycle.

References

\insertRef

ABRW24MSCquartets

See Also

TINNIK, labelIntNodes, resolveCycle, combineCycleResolutions

Examples

data(pTableYeastRokas)
out=TINNIK(pTableYeastRokas, alpha=.01, beta=.05)
ToB=labelIntNodes(out$ToB)
resolveLevel1(ToB, pTable=out$pTable, alpha=.01, beta=.05, distance="NANUQ")

MSCquartets documentation built on Oct. 31, 2024, 1:08 a.m.