defineNeighbours: The function will identify the binary string of all possible...

In rSHAPE: Simulated Haploid Asexual Population Evolution

Description

The function will identify the binary string of all possible neighbours to a focal genotype. It is important when querrying the fitness landscape.

Usage

defineNeighbours(func_tmpGenotype, func_tmpDirection,
  func_maxHamming = getOption("shape_max_numMutations"),
  func_sepString = getOption("shape_sepString"),
  func_genomeLength = getOption("shape_genomeLength"))

Arguments

func_tmpGenotype	This is the binary string of the focal genotype for which we want to define possible neighbours.
func_tmpDirection	This is a logical which controls if reversions are allowed (ie: if TRUE sites can revert from mutated to WT)
func_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.
func_sepString	This is a character string used to collapse vectors of characters.
func_genomeLength	The length of the genomes, or number of mutable sites/positions, being simulated.

Value

Vector of all the genotypes in the neighbouring mutational space accessible within 1 mutation event

Examples

# If you had some individuals with a genome length of 10 sites, and an
# individual with no mutations, as well as one with a single mutation at
# position 7, each had a mutant.  This would define the possible one step
# mutational neighbours.  I also allow back mutations
defineNeighbours(c(""), func_tmpDirection = FALSE, func_maxHamming = 1,
                 func_sepString = "_", func_genomeLength = 10)
defineNeighbours(c("7"), func_tmpDirection = FALSE, func_maxHamming = 1,
                 func_sepString = "_", func_genomeLength = 10)
#' # Same idea, but if we allow back-mutations (ie: reversions)
defineNeighbours(c("7"), func_tmpDirection = TRUE, func_maxHamming = 1,
                 func_sepString = "_", func_genomeLength = 10)

rSHAPE documentation built on July 19, 2019, 5:05 p.m.