selectMatingIndividuals: Selecting mating sequences from a pool of sequences

In caggtaagtat/ModCon: Modifying splice site usage by changing the mRNP code, while maintaining the genetic code

Description

Selecting sequences from a pool of nucleotide sequences based in chance and their HZEI integral.

Usage

selectMatingIndividuals(inputGeneration, whoMatesBestPercent=40, whoMatesSemiRandom=20,
whoMatesLuckily=5, clust, increaseHZEI=TRUE)

Arguments

inputGeneration	Character vector of nucleotide sequences
whoMatesBestPercent	Numeric value e.g. 20 (which would mean that sequences with the top 20 percent highest HZEI integral are selected for mating)
whoMatesSemiRandom	Numeric value (is always lower than total number of sequences in input_generation)
whoMatesLuckily	Numeric value (is always lower than total number of sequences in input_generation)
clust	Name of cluster generated with package parallel
increaseHZEI	Logical value of HZEI integral should be increased or decreased during SD degradation. If TRUE, function aims to increase HZEI integral.

Value

Character vector of nucleotide sequences which are selected from an entered vector of nucleotide sequences inputGeneration for creation of filial sequences by recombination. Sequences are selected by different criteria stated by whoMatesBestPercent, whoMatesSemiRandom, whoMatesLuckily and increaseHZEI.

Examples

## Setup cluster
library(parallel)
nCores <- 1
clust <- makeCluster(nCores)
clusterExport(clust, list('getOverlappingVectorsFromVector',
'hex'), envir=environment())
selectMatingIndividuals(c('CGCGATACGCGCGATACG','CGCGATACGTGGGATATT',
'CTAAGCGCTCGCGATACG','CGCGATACGTTAAGCGCT','GACGATAGTCGCGATACG'),
 whoMatesBestPercent=40, whoMatesSemiRandom=1, whoMatesLuckily=1, clust, increaseHZEI=TRUE)

caggtaagtat/ModCon documentation built on March 12, 2021, 4:12 a.m.