Triplet: Reference class to store and manage triplet data.

In Ward9250/HybridCheck: Detection and dating of Recombinant Regions in DNA sequence data

Description

Reference class to store and manage triplet data.

Fields

ContigNames

character vector of length 3, stores the dna names of which the triplet was made.

ContigNumbers

integer vector of length 3, stores the indecies of the sequences that made the triplet.

Methods

blockDate(dnaobj, parameters)

Block Dating method, estimates the ages of blocks detected based on how many mutations are observed in a block and .

blocksNotDated()

Returns TRUE, if the blocks detected have not been tested for significance or had a divergence time estimated.

blocksNotFound()

Returns TRUE, if the tables for block are blank and no block findng has been done.

initialize(sequencenames, fullseqlength, HCDir)

Initializer function, creates an instance of triplet.

noScanPerformed()

Returns TRUE, if the SS analysis table is blank and the informative sites are not known. This is indicative that a scan of the file has not been done yet.

plotBars(plottingSettings)

Method plots the heatmap based graphic of bars, from the sequence similarity scan data.

plotLines(plottingSettings)

Method plots a lineplot using ggplot2 of the sequence similarity data from the scan.

putativeBlockFind(parameters)

DOCSTRING TO BE COMPLETE

tabulateBlocks()

Tabulates the blocks for a triplet.

Ward9250/HybridCheck documentation built on Jan. 30, 2022, 11:01 a.m.