getKEGG {FunctSNP}R Documentation

Extract pathway names using SNP IDs or Gene IDs

Description

Extract gene ID and KEGG pathway name (from Kyoto Encyclopedia of Genes and Genomes) for each gene ID entered. If SNP ID is entered, KEGG pathway name linked to the gene on which the SNP resides is extracted.

Usage

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

Arguments

ids A vector containing either SNP IDs or gene IDs. If no ids are entered ALL KEGG 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
Pathway KEGG pathway name e.g. path:bta01510

Author(s)

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

See Also

setSpecies getGO getProteins

Examples

## Not run: 
snp_ids <- c(42203337,42203338)
gene_ids <- c(280675, 280678)

# Returns KEGG pathway information for snp_ids (Bos taurus species) 
pathways <- getKEGG (snp_ids, id.type="snp", species="bta")
pathways <- getKEGG (snp_ids,"snp","bta")

# Returns KEGG pathway information for snp_ids - uses species set by setSpecies()
pathways <- getKEGG (snp_ids)

# Returns KEGG pathway information for gene_ids - uses species set by setSpecies()
pathways <- getKEGG (gene_ids,id.type="gene")
pathways <- getKEGG (gene_ids,"gene")

# Returns ALL KEGG pathways - uses species set by setSpecies()
pathways <- getKEGG ()

# Extracting columns
# Extract the SNP_ID and KEGG pathway name columns
pathways <- getKEGG (snp_ids)
names <- pathways [,c("SNP_ID","Pathway")]
## End(Not run)

[Package FunctSNP version 1.0-1 Index]