coil {coil}

coil: evaluation of COI-5P barcode data

Description

coil is an R package designed for the cleaning, contextualization and assessment of cytochrome c oxidase I DNA barcode data (COI-5P, or the five prime portion of COI). It contains functions for placing COI-5P barcode sequences into a common reading frame, translating DNA sequences to amino acids and for assessing the likelihood that a given barcode sequence includes an insertion or deletion error. These functions are provided as a single function analysis pipeline and are also available individually for efficient and targeted analysis of barcode data.

Details

coil is built around the custom 'coi5p' object, which takes a COI-5P DNA barcode sequence as input. The package contains functions for: setting a sequence in reading frame, translating the sequence to amino acids and checking the sequence for evidence of insertion or deletion errors

Functions

• coi5p_pipe Run the entire coi5p analysis pipeline for an input sequence.

• coi5p Builds a coi5p class object.

• frame Sets the sequence into a common reading frame

• which_trans_table Suggests a translation table for a taxonomic designation.

• censored_translation Conducts translation, but ambigious codons are translated to placeholders.

• translate Translate a DNA sequence to amino acids.

• indel_check Check to see if an insertion or deletion error is likely.

Data

• example_nt_string String of DNA barcode data used in the package documentation's examples.

• example_barcode_data A dataframe of coi5p barcode data, demonstrating different example cases.

Author(s)

Cameron M. Nugent