CompetePairs: Find the best match pair in cases where ambiguity exists.

In npcooley/SynExtend: Tools for Working With Synteny Objects

Find the best match pair in cases where ambiguity exists.

Description

A relatively simple routine for identifying a “best” pair in cases where many homologous are identified in a single genome-to-genome comparison. Selection is performed with a single collected measure, and can be performed with or without leveraging context of syntenic blocks.

Usage

CompetePairs(SynExtendObject,
             AllowCrossContigConflicts = TRUE,
             By = "PID",
             PollContext = TRUE,
             NormalizeCompetition = TRUE,
             InflationParameter = .975,
             Verbose = FALSE)

Arguments

SynExtendObject	An object of class PairSummaries.
AllowCrossContigConflicts	A logical indicating where pair competition should take place between genomes or contigs.
By	A character vector of length 1 indicating which column in the PairSummaries object to compete pairs with.
PollContext	A logical indicating whether to include the context of block membership in the competition.
NormalizeCompetition	A logical indicating whether or not to unit normalize the measure being used for competition.
InflationParameter	A numeric of length 1 specifying an adjustment for how block context should be penalized, greater than 1 or rewarded, less than 1.
Verbose	Logical indicating whether or not to display a progress bar and print the time difference upon completion.

Details

CompetePairs uses a naive competition based approach to select a “true-est” ortholog in cases where many competing potential orthologs are present in a set of predicted pairs. The returned value is the previous object with two new attributes, “RetainByCompetition” is a vector of logicals specifying which pairs are retained post competition. A second new attribute named “Knockout” is a character vector that identifies –by rowname– the row which knocked out a removed pair.

Value

An object of class PairSummaries.

Author(s)

Nicholas Cooley [e-mail]

See Also

SummarizePairs, NucleotideOverlap, FindSynteny, ExpandDiagonal, ClusterByK

Examples

data("Endosymbionts_Pairs01", package = "SynExtend")

Pairs02 <- CompetePairs(SynExtendObject = Endosymbionts_Pairs01)

npcooley/SynExtend documentation built on Feb. 19, 2025, 5:18 a.m.