syns_on_ncbi: Checks synonyms against GenBank

In FranzKrah/rmycobank: Interface to mycobank.org

Description

Searches which of the synonyms of an input species list are present on GenBank

Usage

syns_on_ncbi(synonyms)

Arguments

synonyms

a vector of class character containing fungal species names

Details

The function searches which of the synonmys are present at GenBank. If you have a species list e.g. from a field study and want to derive sequences from GenBank but only get a subset of the species; then you might ignore the synonyms.

Value

an data.frame with the synomyms and the GIs, if present.

Author(s)

Franz-Sebastian Krah

Examples

# Use the synonyms derived from mycobank (syno_mycobank)
syns <- syno_mycobank(taxon = "Heterobasidion annosum")
gis <- lapply(syns, syns_on_ncbi)
gis

# or any vector of synonyms
synonyms <- c("Heterobasidion annosum", "Polyporus annosus","Polyporus subpileatus",
"Polyporus scoticus","Polyporus makraulos","Polyporus macraulos","Trametes radiciperda",
"Poria macraula","Poria macraula","Polyporus irregularis","Polystictoides fuscus",
"Polyporus atramosus","Polyporus marginatoides","Polyporus atrannosus",
"Heterobasidion annosum f. macraulos")
gi <- syns_on_ncbi(synonyms)

FranzKrah/rmycobank documentation built on May 6, 2019, 5:06 p.m.