getUPtax: getUPtax

View source: R/utils.R

getUPtaxR Documentation

getUPtax

Description

Get UniProt taxonomy information.

Usage

getUPtax(file, candUP, candTax = NULL)

Arguments

file

downloaded file

candUP

candidate UniProt organism identification codes

candTax

candidate taxonomy name

Details

Obtain the list of UniProt organism identification codes, by querying taxonomy or UniProt codes. https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt The file above must be downloaded and specified to file argument.

Value

data.frame consisting of taxonomy name and UniProt IDs

Examples

file <- "speclist.txt"
## Not run: getUPtax(file, candUP="all")

noriakis/wcGeneSummary documentation built on May 31, 2024, 4:42 p.m.