getGO {FunctSNP}R Documentation

Extract gene ontology using SNP IDs or Gene IDs

Description

Extract gene ID, gene ontology (GO) ID, term type, and term name for each gene ID entered. If SNP ID is entered, GO information linked to the gene on which the SNP resides is extracted.

Usage

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

Arguments

ids A vector containing either SNP IDs or gene IDs. If no ids are entered ALL GO 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
GO_ID gene ontology (GO) ID e.g. GO:0005524
Type Term Type e.g. molecular function, biological process or cellular component
Name Term Name e.g. ATP binding

Author(s)

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

See Also

setSpecies getKEGG getProteins

Examples

## Not run: 
snp_ids <- c(29017382,29009975,29011026)
gene_ids <- c(530393)

# Returns GO information for snp_ids (Bos taurus species) 
go <- getGO (snp_ids, id.type="snp", species="bta")
go <- getGO (snp_ids,"snp","bta")

# Returns GO information for snp_ids - uses species set by setSpecies()
go <- getGO (snp_ids)

# Returns GO information for gene_ids - uses species set by setSpecies()
go <- getGO (gene_ids,id.type="gene")
go <- getGO (gene_ids,"gene")

# Returns ALL GO terms - uses species set by setSpecies()
go <- getGO ()

# Extracting columns
# Extract the SNP_ID and GO term name columns
go <- getGO (snp_ids)
terms <- go [,c("SNP_ID","Name")]
## End(Not run)

[Package FunctSNP version 1.0-1 Index]