convertNomenclature: Convert genes identifier nomenclature.

In CHRONOS: CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

Description

Convert genes identifier nomenclature.

Usage

convertNomenclature(ids, org, from, to)

Arguments

ids	Vector of gene identifiers
org	KEGG organism identifier
from	Initial identifier type
to	A vector of final identifier types

Details

EntrezGene ID	'entrezgene'
Ensembl Gene ID	'ensembl_gene_id'
Ensemble Transcript ID	'ensembl_transcript_id'
Ensemble Protein ID	'ensembl_peptide_id'
HGNC ID	'hgnc_id'
HGNC Symbol	'hgnc_symbol'
HGNC Transcript name	'hgnc_transcript_name'
Refseq mRNA ID	'refseq_mrna'
Refseq Protein ID	'refseq_peptide'
UniProt/Swissprot Accession	'uniprot_swissprot_accession'
UniProt/Swissprot ID	'uniprot_swissprot'
UniGene ID	'unigene'
UniProt Genename ID	'uniprot_genename'

Value

Vector of converted gene identifiers

Examples

# Identifiers to be converted
ids <- c('5091', '5105')

# Convert to HGNC ID, Ensembl Gene ID and UniProt Genename ID
from <- 'entrezgene'
to <- c('hgnc_symbol','ensembl_gene_id', 'uniprot_genename')
## Not run: res <- convertNomenclature(ids=ids, org='hsa', from=from, to=to)

CHRONOS documentation built on Nov. 8, 2020, 8:30 p.m.