aa2selfscore

This function return the selfscore from an AAStringSet.

aa2selfscore(aa, scorematrix = "BLOSUM62")

Arguments

aa

AAStringSet [mandatory]

scorematrix

score matrix to use [default: BLOSUM62]

Value

data.frame

See also

XStringSet-class, substitution.matrices

Author

Kristian K Ullrich

Examples

data(woodmouse, package="ape")
#cds2aa(dnabin2dnastring(woodmouse), shorten=TRUE,
#genetic.code=Biostrings::getGeneticCode("2"))
woodmouse |> dnabin2dnastring() |> cds2aa(shorten=TRUE,
genetic.code=Biostrings::getGeneticCode("2")) |> aa2selfscore()
#>            name score
#> No305     No305  1690
#> No304     No304  1699
#> No306     No306  1702
#> No0906S No0906S  1706
#> No0908S No0908S  1705
#> No0909S No0909S  1706
#> No0910S No0910S  1710
#> No0912S No0912S  1705
#> No0913S No0913S  1705
#> No1103S No1103S  1705
#> No1007S No1007S  1706
#> No1114S No1114S  1605
#> No1202S No1202S  1705
#> No1206S No1206S  1705
#> No1208S No1208S  1698