getGenes {FunctSNP} | R Documentation |
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.
getGenes(ids, id.type = c("snp", "gene"), speciesCode)
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()] |
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 |
S. J. Goodswen <Stephen.Goodswen@csiro.au>
setSpecies
getGeneID
getGenesByDist
## 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)