getSNPs {FunctSNP}R Documentation

Extract SNP information using SNP IDs or Gene IDs

Description

Extract chromosome number, chromosomal location (bp), protein coding status, exon/intron status, description of function, and score for each SNP ID entered. If gene ID is entered, information for all SNPs residing on gene is extracted.

Usage

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

Arguments

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

Details

Each SNP is given a score. There are two elements to the score that are summed: (1) a score according to the SNP location with respect to a gene. For example, the SNP is given a maximum score if it resides on an exon region with a non-synonymous effect, (2) a score according to how much supporting information is found. For example, if the SNP is linked to proteins, GO terms, KEGG pathways, QTL regions, and homologous genes, the score is incremented for each linkage. The maximum FunctSNP SNP score = 26. The higher the score the more likely the SNP has a biological function.

In NCBI's dbSNP there is a function classification for SNPs on genes. The table below shows the function classification in the first column and the FunctSNP score value in the second column. For eample, a SNP in FunctSNP is assigned the score 26 (the maximum possible score) - The SNP score is derived as follows: 20 (SNP alters codon to make an altered amino acid) + 1 (SNP is located in a QTL region) + 1 ( Protein information found) + 1 (GO term found) + 1 (KEGG pathway found) + 1 (OMIA information found) + 1 (homologous genes found).


Function Classification                         Score
----------------------------------------------------
Synonymous amino acid change                    20
Changes to STOP codon                           20
Alters codon to make an altered amino acid      20
indel SNP causing frameshift                    20
Protein coding                                  15
Non-synonymous amino acid change                15
Within 3' 0.5kb to a gene                       10
Within 5' 2kb to a gene                         10
Untranslated region                              5
Protein coding: synonymy unknown                 5
3 prime untranslated                             5
5 prime untranslated region                      5
Intron                                           1
Splice-site                                      1
3 prime acceptor dinucleotide                    1
5 prime donor dinucleotide                       1

Value

A dataframe with the following components:

SNP_ID NCBI dbSNP rs# cluster ID
Chr chromosome number
Location SNP chromosomal location (bp)
is_Coding protein coding status 1/0 (1=SNP is on gene that codes for a protein)
is_Exon exon/intron status 1/0 (1=exon, 0=intron)
Function description of function
Score a score determined by FunctSNP

Author(s)

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

See Also

setSpecies

Examples

## Not run: 
snp_ids <- c(29017382,29009975,29011026)
gene_ids <- c(530393)

# Returns SNP information for snp_ids (Bos taurus species)
snps <- getSNPs (snp_ids, id.type="snp", species="bta")
snps <- getSNPs (snp_ids,"snp","bta")

# Returns SNP information for snp_ids - uses species set by setSpecies ()  
snps <- getSNPs (snp_ids)

# Returns SNP information for all SNPs residing on gene_ids - uses species set by setSpecies ()
snps <- getSNPs (gene_ids,id.type="gene")
snps <- getSNPs (gene_ids,"gene")

# Returns ALL SNPs - uses species set by setSpecies ()
snps <- getSNPs ()

# Extracting columns
# Extract the SNP_ID and chromosome columns
snps <- getSNPs (snp_ids)
chr <- snps[,c("SNP_ID","Chr")]
## End(Not run)

[Package FunctSNP version 1.0-1 Index]