This function shows the population names slot from a
DNAStringSet
or an AAStringSet
metadata
information.
popnames(seq)
DNAStringSet
or AAStringSet
[mandatory]
population names from metadata
## load example sequence data
data(iupac, package="MSA2dist")
iupac.aa <- iupac |> cds2aa(shorten = TRUE)
## create poplist
poplist <- list(FRA = grep("Mmd.FRA", names(iupac)),
GER = grep("Mmd.GER", names(iupac)),
IRA = grep("Mmd.IRA", names(iupac)),
AFG = grep("Mmm.AFG", names(iupac)))
iupac.aa <- iupac.aa |> addpop2string(poplist)
popnames(iupac.aa)
#> $FRA
#> [1] "Mmd.FRA.14" "Mmd.FRA.15B" "Mmd.FRA.16B" "Mmd.FRA.18B" "Mmd.FRA.B2C"
#> [6] "Mmd.FRA.C1" "Mmd.FRA.E1" "Mmd.FRA.F1B"
#>
#> $GER
#> [1] "Mmd.GER.TP1" "Mmd.GER.TP121B" "Mmd.GER.TP17-2"
#> [4] "Mmd.GER.TP3-02" "Mmd.GER.TP4a" "Mmd.GER.TP51D"
#> [7] "Mmd.GER.TP7-10F1A2" "Mmd.GER.TP81B"
#>
#> $IRA
#> [1] "Mmd.IRA.AH15" "Mmd.IRA.AH23" "Mmd.IRA.JR11" "Mmd.IRA.JR15"
#> [5] "Mmd.IRA.JR2-F1C" "Mmd.IRA.JR5-F1C" "Mmd.IRA.JR7-F1C" "Mmd.IRA.JR8-F1A"
#>
#> $AFG
#> [1] "Mmm.AFG.396" "Mmm.AFG.413" "Mmm.AFG.416" "Mmm.AFG.424" "Mmm.AFG.435"
#> [6] "Mmm.AFG.444"
#>