Bug in AAToCodon?

[mikegilchrist]

When using AAToCodon, I get the opposite behavior to what I expect with the focal flag. `

> aaList  <- AnaCoDa::aminoAcids()
> for(aa in aaList){
+     codons <- AnaCoDa::AAToCodon(aa, focal = TRUE);
+     nCodons = length(codons);
+     print(c(aa, nCodons, codons))
+ }
[1] "A"   "3"   "GCA" "GCC" "GCG"
[1] "C"   "1"   "TGC"
[1] "D"   "1"   "GAC"
[1] "E"   "1"   "GAA"
[1] "F"   "1"   "TTC"
[1] "G"   "3"   "GGA" "GGC" "GGG"
[1] "H"   "1"   "CAC"
[1] "I"   "2"   "ATA" "ATC"
[1] "K"   "1"   "AAA"
[1] "L"   "5"   "CTA" "CTC" "CTG" "CTT" "TTA"
[1] "M" "0"
[1] "N"   "1"   "AAC"
[1] "P"   "3"   "CCA" "CCC" "CCG"
[1] "Q"   "1"   "CAA"
[1] "R"   "5"   "AGA" "AGG" "CGA" "CGC" "CGG"
[1] "S"   "3"   "TCA" "TCC" "TCG"
[1] "T"   "3"   "ACA" "ACC" "ACG"
[1] "V"   "3"   "GTA" "GTC" "GTG"
[1] "W" "0"
[1] "Y"   "1"   "TAC"
[1] "Z"   "1"   "AGC"
[1] "X" "0"

> for(aa in aaList){
+     codons <- AnaCoDa::AAToCodon(aa, focal = FALSE);
+     nCodons = length(codons);
+     print(c(aa, nCodons, codons))
+ }
[1] "A"   "4"   "GCA" "GCC" "GCG" "GCT"
[1] "C"   "2"   "TGC" "TGT"
[1] "D"   "2"   "GAC" "GAT"
[1] "E"   "2"   "GAA" "GAG"
[1] "F"   "2"   "TTC" "TTT"
[1] "G"   "4"   "GGA" "GGC" "GGG" "GGT"
[1] "H"   "2"   "CAC" "CAT"
[1] "I"   "3"   "ATA" "ATC" "ATT"
[1] "K"   "2"   "AAA" "AAG"
[1] "L"   "6"   "CTA" "CTC" "CTG" "CTT" "TTA" "TTG"
[1] "M"   "1"   "ATG"
[1] "N"   "2"   "AAC" "AAT"
[1] "P"   "4"   "CCA" "CCC" "CCG" "CCT"
[1] "Q"   "2"   "CAA" "CAG"
[1] "R"   "6"   "AGA" "AGG" "CGA" "CGC" "CGG" "CGT"
[1] "S"   "4"   "TCA" "TCC" "TCG" "TCT"
[1] "T"   "4"   "ACA" "ACC" "ACG" "ACT"
[1] "V"   "4"   "GTA" "GTC" "GTG" "GTT"
[1] "W"   "1"   "TGG"
[1] "Y"   "2"   "TAC" "TAT"
[1] "Z"   "2"   "AGC" "AGT"
[1] "X"   "3"   "TAA" "TAG" "TGA"

> package_info("AnaCoDa")
 package * version date       lib source        
 AnaCoDa   0.1.4.0 2021-06-15 [1] local         
 mvtnorm   1.1-1   2020-06-09 [2] CRAN (R 3.6.3)
 Rcpp      1.0.6   2021-01-15 [1] CRAN (R 3.6.3)
 VGAM      1.1-4   2020-10-23 [2] CRAN (R 3.6.3)

[mikegilchrist]

Suggest changing parameter focal to 'exclude.reference. Value forfocal` used in AAToCodonRange() as forParamVector which, when TRUE, does NOT return the reference or 'focal' parameter

[mikegilchrist]

Still need to do this, so confused as to how plotting code runs with this error.