fetch_conversion_table: Fetches conversion table form one type of identifiers to...

In MSnID: Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications

Description

A wrapper function over AnnotationHub that helps to convert from one protein identifiers to another.

Usage

    fetch_conversion_table(organism_name, 
                           from, to, 
                           backend="AnnotationHub", 
                           snapshot_date=NULL)

Arguments

organism_name	(string) official organism name. E.g. "Homo sapiens", "Mus musculus" or "Rattus norvegicus".
from, to	(string) identifier names. Recommended names are "SYMBOL", "UNIPROT", "REFSEQ" and "ENSEMBLPROT". Other identifiers are possible, but use them at your own risk.
backend	(string) currently only AnnotationHub
snapshot_date	(string) snapshot date for AnnotationHub. Default is NULL meaning latest date.

Value

data.frame with first column name of from identifier, the second name of to identifier

Author(s)

Vladislav A Petyuk [e-mail]

Examples

conv_tbl <- fetch_conversion_table("Rattus norvegicus", "REFSEQ", "SYMBOL")
head(conv_tbl)
conv_tab <- fetch_conversion_table("Homo sapiens", "UNIPROT", "SYMBOL")
head(conv_tbl)

MSnID documentation built on Nov. 8, 2020, 8:03 p.m.