getHomolo {FunctSNP}R Documentation

Extract homologous genes using SNP IDs or Gene IDs

Description

Extract gene ID, gene set ID, gene symbol, protein ID, protein GI, taxonomy ID, and taxonomy name for each SNP ID entered which is on a gene linked to homologous genes. If gene ID is entered, homologous gene information for gene is extracted.

Usage

getHomolo(ids, id.type = c("snp", "gene"), speciesCode, taxon.list = FALSE, taxon.ids)

Arguments

ids A vector containing either SNP IDs or gene IDs. If no ids are entered ALL homologous genes are returned.
id.type Either "snp" or "gene" [Default = "snp"]
speciesCode A 3 letter species code [Default = the species code set by setSpecies()]
taxon.list TRUE or FALSE [Default = FALSE]
taxon.ids A vector containing taxonomy IDs. If no ids are entered ALL species are returned.

Details

A taxon ID may be entered if homologous genes to a specific species are required. A display of taxonomy IDs and taxonomy names for all species can be obtained using taxon.list=TRUE.

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 set the group number to which the gene id belongs
Gene_Symbol gene symbol
Protein_GI NCBI Protein GI number
Protein_ID NCBI Protein ID (Accession number)
Taxon_ID taxonomy ID
Taxon_Name taxonomy name

Author(s)

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

See Also

setSpecies

Examples

## Not run: 
snp_ids <- c(29017382,29009975,29011026)
gene_ids <- c(505968)
taxons<- c(9606,10090)

# Display taxonomy IDs and taxonomy names for all species 
getHomolo(taxon.list=TRUE)

# Returns homologous genes for all taxonomy IDs for snp_ids only if snp resides on gene - uses species set by setSpecies()
homolo <-getHomolo (snp_ids,id.type="snp")
homolo <-getHomolo (snp_ids)

# Returns homologous genes for specified taxonomy IDs for snp_ids only if snp resides on gene - uses species set by setSpecies()
homolo <-getHomolo (snp_ids,taxon.ids="9606,10090")
homolo <-getHomolo (snp_ids,taxon.ids=taxons)

# Returns homologous genes for all taxonomy IDs for snp_ids only if snp resides on gene (accesses the Gallus gallus database)
homolo <-getHomolo (snp_ids, speciesCode="gga")

# Returns homologous genes for all taxonomy IDs for gene_ids - uses species set by setSpecies()
homolo <-getHomolo (gene_ids,id.type="gene")

# Returns homologous genes to specified taxonomy IDs for gene_ids - uses species set by setSpecies()
homolo <-getHomolo (gene_ids,id.type="gene",taxon.ids=taxons)

# Returns homologous genes to all taxonomy IDs for gene_ids(accesses the species Gallus gallus)
homolo <-getHomolo (gene_ids,id.type="gene",species ="gga")

# Returns all homologous genes - uses species set by setSpecies()
homolo <-getHomolo ()

# Extracting columns
# Extract the Gene_ID and gene symbol columns
homolo <-getHomolo (gene_ids,id.type="gene")
sym <- homolo[,c("Gene_ID","Gene_Symbol")]
## End(Not run)

[Package FunctSNP version 1.0-1 Index]