getGeneID {FunctSNP}R Documentation

Extract gene ID information using SNP IDs or SNP locations

Description

Extract gene ID for each SNP ID or SNP chromosomal location (bp) entered, which resides on a gene.

Usage

getGeneID(ids, id.type, speciesCode, loc.keep = TRUE, snpid.keep = TRUE)

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 "loc" [Default = "snp"]
speciesCode A 3 letter species code [Default = the species code set by setSpecies()]
loc.keep return gene ID and SNP location [Default = TRUE (if false returns only Gene ID with SNP ID)]
snpid.keep return gene ID and SNP ID [Default = TRUE (if false returns only Gene ID with SNP Location)]

Value

A dataframe with the following components:

Gene_ID NCBI gene ID
SNP_ID NCBI dbSNP rs# cluster ID (only if snpid.keep = TRUE)
Location SNP chromosomal location (only if loc.keep = TRUE)

Author(s)

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

See Also

setSpecies getGenes getGenesByDist

Examples

## Not run: 
snp_ids <- c(29017382,29009975,29011026)
locs <- c(265772,33635700)

# Returns gene ID with SNP ID and SNP location for SNP locations found on a gene - uses species set by setSpecies()
geneids <- getGeneID (locs,id.type="loc")

# Returns only gene ID with SNP ID if entered location is on a gene - uses species set by setSpecies()
geneids <- getGeneID  (locs,id.type="loc",loc.keep=FALSE)

# Returns gene ID with SNP ID and SNP location if entered SNP ID is on a gene - uses species set by setSpecies()
geneids <- getGeneID  (snp_ids,id.type="snp")
geneids <- getGeneID  (snp_ids)

# Returns gene ID with SNP ID and SNP Location for SNP IDs found on a gene(Bos taurus species)
geneids <- getGeneID  (snp_ids,species="bta")

# Returns ALL gene IDs with SNP ID and SNP location - uses species set by setSpecies()
geneids <- getGeneID () 
## End(Not run)

[Package FunctSNP version 1.0-1 Index]