globalDeletionAA: globalDeletionAA

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

globalDeletionAA

Description

This function returns an AAStringSet reduced by all sites containing any gaps ("-", "+", ".") or missing ("X") sites.

Usage

globalDeletionAA(aa)

Arguments

aa	AAStringSet [mandatory]

Value

AAStringSet

Author(s)

Kristian K Ullrich

Examples

## define two cds sequences
cds1 <- Biostrings::DNAString("ATGCAACATTGC")
cds2 <- Biostrings::DNAString("ATG---CATTGC")
cds1.cds2.aln <- c(Biostrings::DNAStringSet(cds1),
    Biostrings::DNAStringSet(cds2))
#globalDeletionAA(cds2aa(cds1.cds2.aln))
cds1.cds2.aln |> cds2aa() |> globalDeletionAA()

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