getHomolo {FunctSNP} | R Documentation |
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.
getHomolo(ids, id.type = c("snp", "gene"), speciesCode, taxon.list = FALSE, taxon.ids)
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. |
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.
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 |
S. J. Goodswen <Stephen.Goodswen@csiro.au>
## 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)