getTraits {FunctSNP}R Documentation

Extract traits associated with QTL regions using SNP IDs or Gene IDs

Description

Extract SNP ID, trait description associated with quantitative trait loci (QTL) region, and start and end of QTL region for each SNP ID entered. If gene ID is entered, QTL information for each SNP residing on gene is extracted.

Usage

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

Arguments

ids A vector containing either SNP IDs or gene IDs. If ids are entered ALL trait 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
Gene_ID NCBI gene ID
Trait trait description
QTL_Start chromosomal start of the QTL region (bp)
QTL_Stop chromosomal end of the QTL region (bp)

Note

The source of the QTL data is from Animal Quantitative Trait Locus database (QTLdb) - (http://www.animalgenome.org/QTLdb/). Therefore the getTraits() function has no relevance to species not found in QTLdb e.g. Homo sapiens

Author(s)

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

See Also

setSpecies getOMIA

Examples

## Not run: 
snp_ids <- c(17870224,17870268,17870266)
gene_ids <- c(538529)

# Returns QTL trait information for snp_ids (Bos taurus species) 
traits <- getTraits (snp_ids, id.type="snp", species="bta")
traits <- getTraits (snp_ids,"snp","bta")

# Returns QTL trait information for snp_ids - uses species set by setSpecies()  
traits <- getTraits (snp_ids)

# Returns QTL trait information for gene_ids - uses species set by setSpecies() 
traits <- getTraits (gene_ids,id.type="gene")
traits <- getTraits (gene_ids,"gene")

# Returns ALL QTL traits - uses species set by setSpecies()  
traits <- getTraits ()

# Extracting columns
# Extract the SNP_ID and trait description name columns
traits <- getTraits (snp_ids)
trait_desc <- traits [,c("SNP_ID","Trait")]
## End(Not run)

[Package FunctSNP version 1.0-1 Index]