MSCquartets (version 3.1)

resolveLevel1: 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 ABRW24;textualMSCquartets.

Usage

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

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.

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.

References

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")