changeSequenceHZEI {ModCon} | R Documentation

## Adjust HZEI integral of nucleotide sequence

### Description

Adjust the HZEI integral of a nucleotide sequence (min. 24nt long)

### Usage

    changeSequenceHZEI(inSeq, increaseHZEI=TRUE, nGenerations=50, parentSize=300,
    startParentSize=1000, bestRate=50, semiLuckyRate=20, luckyRate=5, mutationRate=1e-04,
    optiRate=100, sdMaximalHBS=10, acMaximalMaxent=4, nCores=-1)

### Arguments

`inSeq` | Character value of nucleotide sequence (min 24nt long, only bases A, G, T or C)
`increaseHZEI` | Logical value if HZEI integral should be increased or decreased during SD degradation. If TRUE, function aims to increase HZEI integral.
`nGenerations` | Numeric value setting maximal number of generations
`parentSize` | Numeric value setting size of parent generations, generated from previous generations
`startParentSize` | Numeric value setting size of initiated parent generation of sequences
`bestRate` | Numeric value setting percentage how many of the fittest sequences are used to produce the next generation
`semiLuckyRate` | Numeric value setting percentage of sequences which are selected for breeding with a probability based on the respective HZEI-score integral
`luckyRate` | Numeric value setting percentage of sequences which are randomly selected for breeding
`mutationRate` | Numeric value setting chance of each codon, to mutate randomly within a child sequence
`optiRate` | Numeric value setting level of HZEI integral optimization
`sdMaximalHBS` | Numeric value of minimal HBS of SDs which should be tried to be degraded in their intrinsic strength
`acMaximalMaxent` | Numeric value of minimal MaxEntScan score of SAs which should be tried to be degraded in their intrinsic strength
`nCores` | Numeric value setting number of cores which should be used for parallel computations. If set to '-1' all availible cores are selected.

### Value

Character value of a nucleotide sequence encoding the same amino acid sequence as `inSeq`, but an increased HZEI integral, due to alternative codon selection.

### Examples

    ## Load R packages
    library('parallel')
    library('utils')
    library('data.table')

    ## Set parameters for genetic algorithm
    inSeq <- 'ATGGAAGACGCCAAAAACATAAAGAAAGGCCCGGCGCCATTCTATCCGCTGGAAGATGGAACC'

    ## Increase HZEI integral
    res <- changeSequenceHZEI(inSeq)

    ## Setting additional parameters
    res <- changeSequenceHZEI(inSeq, increaseHZEI=TRUE, nGenerations=50, parentSize=300,
    startParentSize=1000, bestRate=50, semiLuckyRate=20, luckyRate=5, mutationRate=1e-04,
    optiRate=100, sdMaximalHBS=10, acMaximalMaxent=4, nCores=1)

    ## Access sequence with highest generated HZEI intregral
    res[[3]]

[Package ModCon version 1.0.0 Index]