read.BayesANT.data: Function to import DNA sequences data in the format required...

In alessandrozito/BayesANT: Bayesian Nonparametric Taxonomic classifier

Function to import DNA sequences data in the format required by BayesANT.

Description

Function to import DNA sequences data in the format required by BayesANT.

Usage

read.BayesANT.data(fasta.file, rank = NULL, rank_names = NULL, sep = ";")

Arguments

fasta.file	File in .fas or .fasta format containing the DNA sequences. The correct format for the annotation in the file should start with the ID of the sequence, followed by a space and the word Root;. For example, >COLFF973-13 Root;Arthropoda;Insecta;Coleoptera is an annotation of 3 levels for the reference sequence with ID COLFF973-13.
rank	Numeric argument indicating the number of taxonomic ranks used to construct the library. Counting starts after the Root; in the annotation names. Default is rank = NULL, which automatically selects the lowest level in the loaded taxonomy (the maximum length of the annotations).
rank_names	Names for the taxonomic ranks, eg. "Class" or "Species". Default is rank_names = NULL, which automatically labels the selected ranks as "Level1" up to level "Levelx", where "x" is the value of the parameter rank.
sep	Pattern in the fasta file to separate the rank. Ususally, we have ';', but consider also using '\s+|\|'

Value

An object of class c("data.frame", "BayesANT.data")

alessandrozito/BayesANT documentation built on April 5, 2025, 6:22 a.m.