getOMIA {FunctSNP}R Documentation

Extract OMIA using SNP IDs or Gene IDs

Description

Extract Online Mendelian Inheritance in Animals (OMIA) information for each gene ID entered. If SNP ID is entered, OMIA information linked to the gene on which the SNP resides is extracted

Usage

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

Arguments

ids A vector containing either SNP IDs or gene IDs. If no ids are entered ALL OMIA 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
Defect Phenotype Considered a Defect (Yes or No)
single_Locus Single locus (Yes or No)
Characterised Characterised at a molecular level (Yes or No)
Marker DNA marker e.g. SNP, microsatellite
Symbol Phene symbol e.g. MFS (for Marfan syndrome)
Inherit_Name e.g. Autosomal Recessive, Y-Linked
Phene_Name Phene name e.g. Bovine spongiform encephalopathy
Clin_Feat Clinical Feature e.g. affected calves show cutaneous lesions
Map_Info Map information e.g. 11q28
History e.g. disorder first described in cattle by Testoni et al. (2008)
Pathology e.g. histopathological findings are nonspecific
Prevalence e.g. reported in Denmark, the USA, and the UK
Mol_Gen Molecular genetics e.g. a missense mutation
Control e.g. control of alpha mannosidosis in Angus and Murray Grey cattle
Gen_Test Genetic test e.g. PCR genotyping tests
Summary

Author(s)

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

See Also

setSpecies getTraits

Examples

## Not run: 
snp_ids <- c(17871743,42343650) 
gene_ids <- c(281877)

# Returns OMIA information for snp_ids only if snp on gene - uses species set by setSpecies()
omia <- getOMIA (snp_ids,id.type="snp")
omia <- getOMIA (snp_ids)

# Returns OMIA information for snp_ids only if snp on gene (Gallus gallus species) 
omia <- getOMIA (snp_ids, species="gga")

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

# Returns OMIA information for gene_ids(Gallus gallus species)
omia <- getOMIA (gene_ids,id.type="gene",species ="gga")

# Returns ALL OMIA information - uses species set by setSpecies()
omia <- getOMIA ()

# Extracting columns
# Extract the SNP_ID and Phenotype name columns
omia <- getOMIA (snp_ids)
names <- omia [,c("SNP_ID","Phene_Name")]
## End(Not run)

[Package FunctSNP version 1.0-1 Index]