degradeSAs {ModCon} | R Documentation

## Remove or degrade intrinisc strength of splice acceptors while adjusting HZEI integral.

### Description

Degrade or remove splice acceptor sites of certain intrinsic strength (in MaxEntScan score) from a coding sequence by codon selection while keeping the HZEI integral up.

### Usage

    degradeSAs(fanFunc, maxhbs=10, maxME=4, increaseHZEI=TRUE)

### Arguments

`fanFunc` | codon matrix with two rows (see example below)
`maxhbs` | Numeric treshold which strength of internal donor sites should be degraded (in HBS)
`maxME` | Numeric treshold which strength of internal acceptor sites should be degraded (in MaxEntScan score)
`increaseHZEI` | Logical value if HZEI integral should be increased or decreased during SD degradation. If TRUE, function aims to increase HZEI integral.

### Value

Character value of a nucleotide sequence encoding the same amino acid as the entered codon matrix `fan`, but the intrinsic strength of all present splice acceptor (SA) sites is degraded as much as possible, in case they exceed the given treshold `maxME`. Additionally, splice donor site strengths greater `maxhbs` are avoided, during SA degradation.

### Examples

    library(data.table)
    sdMaximalHBS <- 10
    acMaximalMaxent <- 4
    increaseHZEI <- TRUE
    ## Initiaing the Codons matrix plus corresponding amino acids
    ntSequence <- 'TTTTGTCTTTTTCTGTGTGGCAGTGGGATTAGCCTCCTATCGATCTATGCGATA'
    ## Create Codon Matrix by splitting up the sequence by 3nt
    fanFunc <- createCodonMatrix(ntSequence)
    degradeSAs(fanFunc, maxhbs=sdMaximalHBS, maxME=acMaximalMaxent, increaseHZEI=increaseHZEI)

[Package ModCon version 1.0.0 Index]