addpop2string: addpop2string

In kullrich/MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

addpop2string

Description

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!

Usage

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

Author(s)

Kristian K Ullrich

See Also

addmask2string, addregion2string, addpos2string

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"))$pop.integer
iupac.aa |> popinteger()
#(iupac.aa |> slot("metadata"))$pop.names
iupac.aa |> popnames()
## 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()
iupac.aa |> popnames()
## 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()
iupac.aa |> popnames()

kullrich/MSA2dist documentation built on Nov. 14, 2024, 5:39 p.m.