auditOnID: auditOnID

In Ulises-Rosas/boldminer: Wrapper for BOLD API and DNA barcode auditing

Description

This function adds an audition step (Oliveira et al 2016) to each selected specimen by ID_engine, given a certain threshold. This function, in turn, uses another function called AuditionBarcodes. This prior function is coupled with addAudition and can validate species names by taking accepted names from Worms database.

Usage

auditOnID(seqs, threshold = 0.99, exclude_ncbi = TRUE,
  just_ID = FALSE, make_blast = FALSE, validate_name = FALSE)

Arguments

seqs	sequence file
threshold	minimal similarity proportion allowed between sample and specimen matches
exclude_ncbi	exclude barcodes obtained from NCBI when DNA barcode auditing is allowed, i.e. not just_ID
just_ID	if TRUE, audition step is skipped
make_blast	if TRUE, blastn algorithm is run for matching sequences
validate_name	if TRUE, validation of species name is performed. This validation of name is performed by using taxamatch algorithm from http://www.marinespecies.org/aphia.php?p=webservice

Value

species ID plus DNA barcode auditing

Examples

## Not run: 
seqs  = system.file("sequences.fa", package = "boldminer")
boldminer::auditOnID(seqs, just_ID = TRUE)


## End(Not run)

Ulises-Rosas/boldminer documentation built on Dec. 18, 2019, 2:53 a.m.