getGenes {FunctSNP}R Documentation

Extract gene information using SNP IDs or Gene IDs

Description

Extract gene ID, gene symbol, chromosome number, chromosome arm location, start and end location, and gene name for each gene ID entered. If SNP ID is entered, information for the gene on which the SNP resides is extracted.

Usage

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

Arguments

ids A vector containing either SNP IDs or gene IDs. If no ids are entered ALL genes are 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
Gene_Symbol gene symbol
Gene_Chr chromosome number on which the gene resides
Gene_Chr_Arm chromosome arm on which the gene resides e.g. 5q35
Gene_Start chromosomal gene start position (bp)
Gene_Stop chromosomal gene stop position (bp)
Gene_Name gene name

Author(s)

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

See Also

setSpecies getGeneID getGenesByDist

Examples

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

# Returns gene information for snp_ids (Bos taurus species) if snp resides on gene
genes <- getGenes (snp_ids, id.type="snp", species="bta")
genes <- getGenes (snp_ids,"snp","bta")

# Returns gene information for snp_ids - uses species set by setSpecies()   
genes <- getGenes (snp_ids)

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

# Returns ALL genes - uses species set by setSpecies()  
genes <- getGenes ()

# Extracting columns
# Extract the Gene_ID and gene name columns
genes <- getGenes (snp_ids)
name <- genes[,c("Gene_ID","Gene_Name")]
## End(Not run)

[Package FunctSNP version 1.0-1 Index]