alignedForUnalignedAAPos: Computes the position of the unaligned character at argument...

In asishallab/GeneFamilies: Analyses different properties of gene families

Computes the position of the unaligned character at argument position 'char.pos' in the aligned sequence of argument 'gene'.

Description

Computes the position of the unaligned character at argument position 'char.pos' in the aligned sequence of argument 'gene'.

Usage

alignedForUnalignedAAPos(gene, char.pos, msa.fasta,
  gap.char = getOption("GeneFamilies.gap.char", "-"))

Arguments

gene	The gene accession / ID as used in 'msa.fasta'
char.pos	The index of the homologous amino acid subject to selection (integer coordinate)
msa.fasta	The result of seqinr::read.fasta(path_2_AAs_MSA.fasta, seqtype='AA', as.string=TRUE, strip.desc=TRUE).
gap.char	The character used to identify non sequence characters in the aligned sequences. Default is getOption('GeneFamilies.gap.char', '-').

Value

An integer; either NA if the position is a non sequence character, or the corresponding aligned position.

asishallab/GeneFamilies documentation built on May 22, 2023, 11:30 a.m.