R/phyloscan.fun.R
phsc.find.transmission.networks.from.linked.pairs.Rd
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.
phsc.find.transmission.networks.from.linked.pairs(rtp, rplkl, conf.cut = conf.cut, neff.cut = neff.cut, verbose = TRUE)
rtp | Pairs of individuals between whom linkage is not excluded, stored as data.table. |
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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. |
list of two R objects 'transmission.networks', 'most.likely.transmission.chains'. See description.