geneHapR (version 1.2.4)

import_MultipleAlignment: Import MultipleAlignment Result

Description

import sequences algned results

Usage

import_MultipleAlignment(filepath, format = "fasta", type = "DNA")

Value

object of DNAMultipleAlignment

Arguments

filepath

A character vector (of arbitrary length when reading, of length 1 when writing) containing the paths to the files to read or write. Note that special values like "" or "|cmd" (typically supported by other I/O functions in R) are not supported here. Also filepath cannot be a connection.

format

Either "fasta" (the default), stockholm, or "clustal".

type

one of "DNA" and "Protein"

Examples

aliSeqPath <- system.file("extdata", "seqs.fa", package = "geneHapR")

geneSeqs <- import_MultipleAlignment(filepath = aliSeqPath,
                                     format = "fasta",
                                     type = "DNA")
geneSeqs <- import_MultipleAlignment(filepath = aliSeqPath,
                                     format = "fasta",
                                     type = "Protein")