addpop2string

This function adds population information to a DNAStringSet or an AAStringSet and puts them into the metadata information.
__Note__: All unassigned sequences will be put into pop "unassigned"!
Do not use "unassigned" as a population name!
__Note__: Names in a population in the poplist must match sequence names!
__Note__: Duplicated assignments are allowed!

addpop2string(seq, poplist)

Arguments

seq

DNAStringSet or AAStringSet [mandatory]

poplist

named list of populations either as index or names per population (do not mix index and names in one population) [mandatory]

Value

An object of class DNAStringSet or AAStringSet

See also

addmask2string, addregion2string, addpos2string

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)
#(iupac.aa |> slot("metadata"))$pop.integer
iupac.aa |> popinteger()
#> $FRA
#> [1] 1 2 3 4 5 6 7 8
#> 
#> $GER
#> [1]  9 10 11 12 13 14 15 16
#> 
#> $IRA
#> [1] 17 18 19 20 21 22 23 24
#> 
#> $AFG
#> [1] 25 26 27 28 29 30
#> 
#(iupac.aa |> slot("metadata"))$pop.names
iupac.aa |> popnames()
#> $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"
#> 
## mxixing index and names
poplist <- list(FRA = names(iupac)[grep("Mmd.FRA", names(iupac))],
    GER = grep("Mmd.GER", names(iupac)),
    IRA = names(iupac)[grep("Mmd.IRA", names(iupac))],
    AFG = grep("Mmm.AFG", names(iupac)))
iupac.aa <- iupac.aa |> addpop2string(poplist)
iupac.aa |> popinteger()
#> $FRA
#> [1] 1 2 3 4 5 6 7 8
#> 
#> $GER
#> [1]  9 10 11 12 13 14 15 16
#> 
#> $IRA
#> [1] 17 18 19 20 21 22 23 24
#> 
#> $AFG
#> [1] 25 26 27 28 29 30
#> 
iupac.aa |> popnames()
#> $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"
#> 
## leaving out some sequences which will be assigned as "unassigned"
poplist <- list(FRA = names(iupac)[grep("Mmd.FRA", names(iupac))],
    GER = grep("Mmd.GER", names(iupac)),
    IRA = names(iupac)[grep("Mmd.IRA", names(iupac))])
iupac.aa <- iupac.aa |> addpop2string(poplist)
iupac.aa |> popinteger()
#> $FRA
#> [1] 1 2 3 4 5 6 7 8
#> 
#> $GER
#> [1]  9 10 11 12 13 14 15 16
#> 
#> $IRA
#> [1] 17 18 19 20 21 22 23 24
#> 
#> $unassigned
#> [1] 25 26 27 28 29 30
#> 
iupac.aa |> popnames()
#> $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"
#> 
#> $unassigned
#> [1] "Mmm.AFG.396" "Mmm.AFG.413" "Mmm.AFG.416" "Mmm.AFG.424" "Mmm.AFG.435"
#> [6] "Mmm.AFG.444"
#>