find_neededNeighbours {rSHAPE}

This function querries if a suite of genotypes exist within the fitness landscape database.

Description

This function querries if a suite of genotypes exist within the fitness landscape database.

Usage

find_neededNeighbours(tmp_possibleNeighbours, tmp_focal_numMuts,
  tmp_refTables, maxHamming = getOption("shape_max_numMutations"),
  tmp_tableSplit = getOption("shape_db_splitTables"),
  tmp_genomeLength = getOption("shape_genomeLength"),
  tmpDirection = getOption("shape_allow_backMutations"),
  tmpRange_numMuts = NULL, tmp_genCon)

Arguments

tmp_possibleNeighbours

This is a vector of all possible mutants that we're trying to querry within the fitness landscape database.

tmp_focal_numMuts

This is the number of mutations in the focal genotype, it controls - along with other parameters - what tables of the fitness landscape database are querried.

tmp_refTables

This is the a vector of named tables that exist within the fitness landscape. It can not be passed in which case the database at tmp_genCon is querried for this information.

maxHamming

The maximum number of sites that could be changed by mutation of the tmp_focalGenotype.

tmp_tableSplit

This is a logical which controls if the tables which report on all genotypes with X mutations should be forced into a single table or it SHAPE is allowed to split them into multiple tables.

tmp_genomeLength

The length of the genomes, or number of mutable sites/positions, being simulated.

tmpDirection

This is a logical which controls if reversions are allowed (ie: if TRUE sites can revert from mutated to WT)

tmpRange_numMuts

This is the range of number of mutations which a mutant neighbour may posses. If not supplied that will be calculated in line via other parameters passed to the function.

tmp_genCon

This is the filepath for the database file that contains the fitness landscape information.

Value

A vector of the genotypes that need to be created as they've not yet been defined within the fitness landscape.

Note

There is no example as this cannot work outisde of a runSHAPE call, it requires data produced by the simulation experiment.