phsc.find.transmission.networks.from.linked.pairs: Find phylogenetic transmission networks

In olli0601/Phyloscanner.R.utilities:

Find phylogenetic transmission networks

Description

This function reconstructs phylogenetic transmission networks from pairs of individuals between whom linkage is not excluded. Two R objects are generated: 'transmission.networks' is a data.table describing transmission networks, with information of phylogenetic support for transmission in direction 12, direction 21, linkage with direction unclear, and no linkage. 'most.likely.transmission.chains' is a data.table describing the most likely transmission chain for each transmission network.

Usage

phsc.find.transmission.networks.from.linked.pairs(
  rtp,
  rplkl,
  conf.cut = conf.cut,
  neff.cut = neff.cut,
  verbose = TRUE
)

Arguments

rtp	Pairs of individuals between whom linkage is not excluded, stored as data.table.
rplkl	Summary of phylogenetic relationship counts for each pair, stored as data.table.
conf.cut	Threshold on the proportion of deep-sequence phylogenies with distant/disconnected subgraphs above which pairs are considered phylogenetically unlinked. Default: 0.6
neff.cut	Threshold on the minimum number of deep-sequence phylogenies with sufficient reads from two individuals to make any phylogenetic inferences. Default: 3.
verbose	Flag to switch on/off verbose mode. Default: TRUE.

Value

list of two R objects 'transmission.networks', 'most.likely.transmission.chains'. See description.

olli0601/Phyloscanner.R.utilities documentation built on April 21, 2024, 1:59 p.m.