ModCon {ModCon} | R Documentation

## ModCon

### Description

Execute ModCon on a donor site within a coding sequnece either increasing or decreasing its HZEI weight.

### Usage

    ModCon(cds, sdSeqStartPosition, upChangeCodonsIn=16, downChangeCodonsIn=16,
    optimizeContext=TRUE, sdMaximalHBS=10, acMaximalMaxent=4, optiRate=100,
    nGenerations=50, parentSize=300, startParentSize=1000, bestRate=40,
    semiLuckyRate=20, luckyRate=5, mutationRate=1e-04, nCores=-1)

### Arguments

`cds` | Character value of coding nucleotide sequence which holds the splice site of interest
`sdSeqStartPosition` | Numeric value of the position of the first nucleotide of the splice donor of interest
`upChangeCodonsIn` | Numeric value of number of codons to change upstream of the donor site of interest
`downChangeCodonsIn` | Numeric value of number of codons to change downstream of the donor site of interest
`optimizeContext` | Character value which determines, if TRUE (the default) the donor context will be adjusted to increase the splice site HEXplorer weight (SSHW), if FALSE, the SSHW will be decreased.
`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
`optiRate` | Numeric value setting level of HZEI integral optimization
`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
`nCores` | Numeric value setting number of cores which should be used for parallel computations. If set to '-1' all availible cores are selected.

### Value

Creates a character value of a coding nucleotide sequence encoding the same amino acid sequence as the entered `cds`, but with an alternative nucleotide surrounding around the splice donor (SD) sequence position, stated with `sdSeqStartPosition`. Depending on the entered `optimizeContext`, the SD surrounding is either adjusted aiming to enhance or decrease the splice site HEXplorer wheigth.

### Examples

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

    ## Set parameters for simplest use of ModCon (optimizing to 100%)
    cds <- paste0('ATGGAAGACGCCAAAAACATAAAGAAAGGCCCGGCGCCATTCTATCCGCTGGAAGATGGAACCGCTGGAGAGCAACTGCA',

    'TAAGGCTATGAAGAGATACGCCCTGGTTCCTGGAACAATTGCTTTTACAGATGCACATATCGAGGTGGACATCACTTACGCTGAGTACTTCGAAA',
    'TGTCCGTTCGGTTGGCAGAAGCTATGAAACGATATGGGCTGAATACAAATCACAGAATCGTCGTATGCAGTGAAAACTCTCTTCAATTCTTTAT',
    'GCCGGTGTTGGGCGCGTTATTTATCGGAGTTGCAGTTGCGCCCGCGAACGACATTTATAATGAACGTGAATTGCTCAACAGTATGGGCATTTCG',
    'CAGCCTACCGTGGTGTTCGTTTCCAAAAAGGGGTTGCAAAAAATTTTGAACGTGCAAAAAAAGCTCCCAATCATCCAAAAAATTATTATCATGG',
    'ATTCTAAAACGGATTACCAGGGATTTCAGTCGATGTACACGTTCGTCACATCTCATCTACCTCCCGGTTTTAATGAATACGATTTTGTGCCAGA',
    'GTCCTTCGATAGGGACAAGACAATTGCACTGATCATGAACTCCTCTGGATCTACTGGTCTGCCTAAAGGTGTCGCTCTGCCTCATAGAACTGCC',
    'TGCGTGAGATTCTCGCATGCCAGAGATCCTATTTTTGGCAATCAAATCATTCCGGATACTGCGATTTTAAGTGTTGTTCCATTCCATCACGGTT',
    'TTGGAATGTTTACTACACTCGGATATTTGATATGTGGATTTCGAGTCGTCTTAATGTATAGATTTGAAGAAGAGCTGTTTCTGAGGAGCCTTCA',
    'GGATTACAAGATTCAAAGTGCGCTGCTGGTGCCAACCCTATTCTCCTTCTTCGCCAAAAGCACTCTGATTGACAAATACGATTTATCTAATTTA',
    'CACGAAATTGCTTCTGGTGGCGCTCCCCTCTCTAAGGAAGTCGGGGAAGCGGTTGCCAAGAGGTTCCATCTGCCAGGTATCAGGCAAGGATATG',
    'GGCTCACTGAGACTACATCAGCTATTCTGATTACACCCGAGGGGGATGATAAACCGGGCGCGGTCGGTAAAGTTGTTCCATTTTTTGAAGCGAA',
    'GGTTGTGGATCTGGATACCGGGAAAACGCTGGGCGTTAATCAAAGAGGCGAACTGTGTGTGAGAGGTCCTATGATTATGTCCGGTTATGTAAAC',
    'AATCCGGAAGCGACCAACGCCTTGATTGACAAGGATGGATGGCTACATTCTGGAGACATAGCTTACTGGGACGAAGACGAACACTTCTTCATCG',
    'TTGACCGCCTGAAGTCTCTGATTAAGTACAAAGGCTATCAGGTGGCTCCCGCTGAATTGGAATCCATCTTGCTCCAACACCCCAACATCTTCGA',
    'CGCAGGTGTCGCAGGTCTTCCCGACGATGACGCCGGTGAACTTCCCGCCGCCGTTGTTGTTTTGGAGCACGGAAAGACGATGACGGAAAAAGAG',
    'ATCGTGGATTACGTCGCCAGTCAAGTAACAACCGCGAAAAAGTTGCGCGGAGGAGTTGTGTTTGTGGACGAAGTACCGAAAGGTCTTACCGGAA',
    'AACTCGACGCAAGAAAAATCAGAGAGATCCTCATAAAGGCCAAGAAGGGCGGAAAGATCGCCGTG')

    ## Execute ModCon
    finalSequence <- ModCon(cds, 1001)

    ## Print final cds sequence with the alternative SD nucleotide surrounding
    print(finalSequence)

    ## More parameters can be set for use of ModCon when not optimizing to 100% (e.g. 50%)

    ## Execute ModCon
    finalSequence <- ModCon(cds, 1001, upChangeCodonsIn=16, downChangeCodonsIn=16,
    optimizeContext=FALSE, sdMaximalHBS=10, acMaximalMaxent=4,
    optiRate=50, nGenerations=5, parentSize=200, startParentSize=800,
    bestRate=50, semiLuckyRate=10, luckyRate=5, mutationRate=1e-03, nCores=1)

    ## Print final cds sequence with the alternative SD nucleotide surrounding
    print(finalSequence)

[Package ModCon version 1.0.0 Index]