This function shows the population names slot from a DNAStringSet or an AAStringSet metadata information.

popnames(seq)

Arguments

seq

DNAStringSet or AAStringSet [mandatory]

Value

population names from metadata

See also

Author

Kristian K Ullrich

Examples

## 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"
#>