createGenotypes {rSHAPE}

This function searches the nearby mutational space of a focal genotype, identifies which genotypes in that space have not yet been identified, and create new database entries for any new genotypes.

Description

This function searches the nearby mutational space of a focal genotype, identifies which genotypes in that space have not yet been identified, and create new database entries for any new genotypes.

Usage

createGenotypes(tmp_focalGenotype, tmp_focalFitness, maxHamming,
  tmp_landModel = "HoC", tmp_sepString = getOption("shape_sepString"),
  tmpDirection = getOption("shape_allow_backMutations"),
  tmp_relativeFitness = getOption("shape_const_relativeFitness"),
  tmp_currNeighbours = NULL, tmp_genCon,
  tmp_tableSplit = getOption("shape_db_splitTables"),
  tmp_maxRows = getOption("shape_maxRows"),
  tmp_genomeLength = getOption("shape_genomeLength"),
  tmp_distAsS = getOption("shape_const_distAsS"), ...)

Arguments

tmp_focalGenotype

This is the focal genotype for which we want to create missing mutational neighbours.

tmp_focalFitness

This is the fitness value of the tmp_focalGenotype.

maxHamming

The maximum number of sites that could be changed by mutation of the tmp_focalGenotype. NOTE: At present I've not made the code work for anything other than a value of 1. So do not update without updating associated code. where appropriate.

tmp_landModel

This is the character string that defines the fitness landscape model being simulated in this SHAPE run. At present it can be one of: Additive, Fixed, HoC, NK, RMF

tmp_sepString

This is a character string used to collapse vectors of characters.

tmpDirection

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

tmp_relativeFitness

This is a logical which controls if fitness values are to be calculated as relative and no absolute values that would otherwise be calculated via calls to the fitness landscape model.

tmp_currNeighbours

This is an optinal vector that would define the genotype of all neighbours within the 1 step mutational neighbourhood of the tmp_focalGenotype genotype. If NULL then this vector will be calculated within the function.

tmp_genCon

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

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_maxRows

The maximum number of rows allowed in a database table before a new table is created. This has no meaning if tmp_tableSplit is FALSE.

tmp_genomeLength

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

tmp_distAsS

This arugment is passed through to downstream function, but will control if the stochastic portion of fitness effect will be considered as selection coefficients (meaning subtracting 1 from the initially drawn value).

...

Additional arguments that may get passed to internal functions.

Value

This invisibly returns NULL, this function is to perform work on databases.

Note

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