degradeSAs {ModCon} | R Documentation |
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.
degradeSAs(fanFunc, maxhbs=10, maxME=4, increaseHZEI=TRUE)
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. |
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.
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)