popinteger: popinteger

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

popinteger

Description

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

Usage

popinteger(seq)

Arguments

seq	DNAStringSet or AAStringSet [mandatory]

Value

population integer from metadata

Author(s)

Kristian K Ullrich

See Also

addpop2string

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)
popinteger(iupac.aa)

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