changeSequenceHZEI {ModCon} | R Documentation |
Adjust the HZEI integral of a nucleotide sequence (min. 24nt long)
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)
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. |
Character value of a nucleotide sequence encoding the same amino acid sequence as inSeq
, but an increased HZEI integral, due to alternative codon selection.
## 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]]