requestPomacanthidaeBOLD: BOLD (Barcode of Life) specimen + sequence data with matching...
In Grelot/geogendivr: Geographic Gene Diversity in R

Description Usage Format Details Source References

A list of lists returned by bold_seqspec command from bold package. They are 2 lists: specimen information (spatial coordinates, taxonomy...) and DNA barcode sequences.

Each row is related to an individual sequences. They are 725 published records, with 725 records with sequences, forming 71 BINs (clusters), with specimens from 46 countries, deposited in 27 institutions.

Of these records, 687 have species names, and represent 70 species.

We use this dataset as an example to test functions of package geogendivr.

data(resBold)
## specimen data
resBold$data
## fasta sequences
resBold$fasta
## mutate and filter dataset
prparedResBold <- prepare_bold_res(resBold,
                                   marker_code="COI-5P",
                                   species_names=TRUE,
                                   coordinates=TRUE,
                                   ambiguities=TRUE,
                                   min_length=420,
                                   max_length=720
                                   )

A list which contains 2 lists with 725 observations.

data

a list of specimen information (80 fields) such as :

processid an integer identifier for DNA sequences
lat float degree latitude coordinates
lon float degree longitude coordinates
region string geographical region
marker_codes string mitochondrial region barcode
species_name string taxonomy species
genus_name string taxonomy genus
family_name string taxonomy family
order_name string taxonomy order
class_name string taxonomy class
...

fasta

a list of sequences

We generated this dataset using the following command with bold package, the 6th march 2020: resBold <- bold_seqspec(taxon="Pomacanthidae", sepfasta=TRUE)

http://www.boldsystems.org

The Barcode of Life Data System (BOLD) is an online workbench and database that supports the assembly and use of DNA barcode data. It is a collaborative hub for the scientific community and a public resource for citizens at large.

Grelot/geogendivr documentation built on Sept. 3, 2020, 6:25 p.m.