regionused: regionused

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

regionused

Description

This function shows the region used slot from a DNAStringSet or an AAStringSet metadata information.

Usage

regionused(seq)

Arguments

seq	DNAStringSet or AAStringSet [mandatory]

Value

population names from metadata

Author(s)

Kristian K Ullrich

See Also

addpop2string

Examples

## load example sequence data
data("hiv", package="MSA2dist")
## create mask
mask1 <- IRanges::IRanges(start=c(11,41,71), end=c(20,50,80))
## use mask
hiv.region <- hiv |> cds2aa() |> string2region(mask=mask1)
#(hiv.region |> slot("metadata"))$regionUsed
hiv.region |> regionused()

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