WithinSetCompetition: Pare down candidate pairs to one-to-one sets.

In npcooley/SynExtend: Tools for Comparative Genomics

Pare down candidate pairs to one-to-one sets.

Description

This function is a work in progress, please be patient.

Usage

WithinSetCompetition(SynExtendObject,
                     AllowCrossContigConflicts = TRUE,
                     CompeteBy  = "Delta_Background",
                     PollContext = TRUE,
                     ContextInflation = 0.975,
                     Verbose = FALSE)

Arguments

SynExtendObject	A PairSummaries object created by SummarizePairs.
AllowCrossContigConflicts	Logical; return only one candidate per per disjoint set for each contig to contig pair, or for each genome to genome pair.
CompeteBy	Character; a column name from the PairSummaries object.
PollContext	Logical; when competing candidate pairs, consider block membership.
ContextInflation	Numeric; a value to adjust block membership strength. Lower values increase the strength of block membership.
Verbose	Logical; print a progress bar and timings.

Details

For each assembly to assembly comparison, or each contig to contig comparison, all disjoint sets are collected for candidate pairs. In cases where there are more than 2 nodes, i.e. features, in a set, the connecting edges are competed against each other, and only the strongest edges – and their resulting nodes – are retained.

Value

A PairSummaries object.

Author(s)

Nicholas Cooley [e-mail]

See Also

SummarizePairs

Examples

data("Endosymbionts_Pairs01", package = "SynExtend")
x <- WithinSetCompetition(Endosymbionts_Pairs01)

npcooley/SynExtend documentation built on June 8, 2025, 5:24 a.m.