getProteins {FunctSNP}R Documentation

Extract protein information using SNP IDs or Gene IDs

Description

Extract protein ID, UniProt ID, and protein name linked to each gene ID entered. If SNP ID is entered, the protein information linked to the gene on which the SNP resides is extracted.

Usage

getProteins(ids, id.type = c("snp", "gene"), speciesCode)

Arguments

ids A vector containing either SNP IDs or gene IDs. If ids are entered ALL protein information is returned.
id.type Either "snp" or "gene" [Default = "snp"]
speciesCode A 3 letter species code [Default = the species code set by setSpecies()]

Value

A dataframe with the following components:

SNP_ID NCBI dbSNP rs# cluster ID (only if id.type = "snp")
Gene_ID NCBI gene ID
Protein_ID NCBI protein ID (Accession number) e.g. XP_001615462
UniProt_ID UniProt ID e.g. A5K507
Protein_Name protein name

Author(s)

S. J. Goodswen <Stephen.Goodswen@csiro.au>

See Also

setSpecies getGO getKEGG

Examples

## Not run: 
snp_ids <- c(43501919,41603159)
gene_ids <- c(530393)

# Returns protein information for snp_ids (Bos taurus species) 
proteins <- getProteins (snp_ids, id.type="snp", species="bta")
proteins <- getProteins (snp_ids,"snp","bta")

# Returns protein information for snp_ids - uses species set by setSpecies ()
proteins <- getProteins (snp_ids)

# Returns protein information for gene_ids - uses species set by setSpecies ()
proteins <- getProteins (gene_ids,id.type="gene")
proteins <- getProteins (gene_ids,"gene")

# Returns ALL proteins - uses species set by setSpecies ()
proteins <- getProteins ()

# Extracting columns
# Extract the SNP_ID and protein name columns
proteins <- getProteins (snp_ids)
names <- proteins [,c("SNP_ID","Protein_Name")]
## End(Not run)

[Package FunctSNP version 1.0-1 Index]