ComputeCarboneRA: Compute Carbone Relative Adaptiveness

In fredysiegrist/statanacoseq: Statistical Analyses of Codon Usage in Custom Genome Sequences

Description

ComputeCarboneRA calculates RA

Usage

ComputeCarboneRA(target = 0.05, initfrac = 1, iterfrac = 0.5,
  reverse = FALSE, DB = mylist(whatout = 1))

Arguments

target	nonnegative
initfrac	nonnegative
reverse	For standard anything else for non-standard
DB	Database with working genes of type Entires()
interfrac	nonnegative

Details

Should compute the same RA in Darwin

Value

Named (codons) numerical vector with relative synonymous codon usage for the 64 codons

Original code in Darwin

Compute Carbone Relative Adaptiveness

ComputeCarboneRA := proc( ; t=0.01:nonnegative, initfrac=1:nonnegative, iterfrac=0.5:nonnegative, mode:string)
 global RA;
 if not assigned(DB) then error('DB must be assigned') fi;
 x := 1;  # fraction of the sequences used to compute RA in this iteration
 AllGenes := [seq(i, i=1..DB[TotEntries])]:
 genes := Shuffle(AllGenes)[1..round(initfrac * DB[TotEntries])]:
 bestCorr := 0;
 cai := CreateArray(1..DB[TotEntries]):
 while length(genes) / DB[TotEntries] > t do
   RA := RelativeAdaptiveness(genes);
   for i to DB[TotEntries] do
     dna:=SearchTag('DNA',Entry(i));
     if SearchString('X', dna)<>-1 then next fi;
     cai[i] := ComputeCAI(dna) od;
   x := x * iterfrac;
   res := transpose([AllGenes, cai]):
   if mode='reverse' then
     res := transpose(sort(res, res -> res[2])):
   else
     res := transpose(sort(res, res -> -res[2])):
   fi;
   genes := res[1][1..round(x * DB[TotEntries])]:
 od;
RA
end: 

Author(s)

Roth, A.; Friberg, M.; Siegrist, F. and Cannarozzi, G. M. [e-mail]

See Also

RelativeAdaptiveness statanacoseq SetupRA Entries

Examples

ComputeCarboneRA(DB=mylist(whatout=1))

fredysiegrist/statanacoseq documentation built on May 16, 2019, 2:44 p.m.