In jailagolden/package: Map organisms in the World map.

knitr::opts_chunk$set(echo = TRUE)

This function obtains fasta files from the NCBI database.

To use it first you have to perform a search from the database before you execute the function. The search results are then stored in a list. You might want to login to your NCBI account and obtain the api key. You can follow https://www.ncbi.nlm.nih.gov/account/settings/ this link and it should be under API management. Instead of "genus" you can use any genus to obtain the fasta files.

search <-  entrez_search(db = "Nucleotide", term="Quelea", retmax = 100, api_key ="669d671ec088301f59dc01dd767127db2508")

Then, to obtain the fasta files just use the following command.

fasta("Quelea")

The downloaded fasta files will be present in the root of the working directory as genus.fasta file.This can be used for any further analyses.

jailagolden/package documentation built on Jan. 1, 2021, 4:26 a.m.