coil: 'coil': evaluation of COI-5P barcode data
In coil: Contextualization and Evaluation of COI-5P Barcode Data

coil	R Documentation

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.