artmsAnnotationUniprot: Annotate table with Gene Symbol and Name based on Uniprot...

In kroganlab/artMS: Analytical R tools for Mass Spectrometry

Annotate table with Gene Symbol and Name based on Uniprot ID(s)

Description

Annotate gene name and symbol based on uniprot ids. It will take the column from your data.frame specified by the columnid argument, search for the gene symbol, name, and entrez based on the species (species argument) and merge the information back to the input data.frame

Usage

artmsAnnotationUniprot(x, columnid, species, verbose = TRUE)

Arguments

x	(data.frame) to be annotated (or file path and name)
columnid	(char) The column with the uniprotkb ids
species	(char) The species name. Check ?artmsMapUniprot2Entrez to find out more about supported species.
verbose	(logical) TRUE (default) shows function messages

Value

(data.frame) with two new columns: Gene and Protein.name

Examples

# This example adds annotations to the example evidence file included in
# artMS, based on the column 'Proteins'.

evidence_anno <- artmsAnnotationUniprot(x = artms_data_ph_evidence,
                                         columnid = 'Proteins',
                                         species = 'human')

kroganlab/artMS documentation built on July 7, 2023, 5:35 a.m.