getGeneID {FunctSNP} | R Documentation |
Extract gene ID for each SNP ID or SNP chromosomal location (bp) entered, which resides on a gene.
getGeneID(ids, id.type, speciesCode, loc.keep = TRUE, snpid.keep = TRUE)
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)] |
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) |
S. J. Goodswen <Stephen.Goodswen@csiro.au>
setSpecies
getGenes
getGenesByDist
## 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)