globalDeletion: globalDeletion

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

globalDeletion

Description

This function returns a DNAStringSet reduced by all sites containing any gaps ("-", "+", ".") or missing ("N") sites.

Usage

globalDeletion(dna)

Arguments

dna	DNAStringSet [mandatory]

Value

DNAStringSet

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))
globalDeletion(cds1.cds2.aln)

kullrich/MSA2dist documentation built on April 26, 2024, 4:43 p.m.