getSNPID {FunctSNP}R Documentation

Extract SNP ID using Gene IDs or SNP locations

Description

Extract SNP ID for each gene ID or SNP chromosomal base pair location entered. If gene ID is entered, SNP IDs for all SNPs residing on gene will be extracted.

Usage

getSNPID(ids=c(), id.type = c("gene","loc"), speciesCode=c(), loc.keep = TRUE, geneid.keep = TRUE)

Arguments

ids A vector containing either gene IDs or SNP base pair locations. If no ids are entered ALL SNP IDs are returned.
id.type Either "gene" or "loc" [Default = "gene"]
speciesCode A 3 letter species code [Default = the species code set by setSpecies ()]
loc.keep return SNP ID and location [Default = TRUE (if false returns only SNP ID with gene ID)]
geneid.keep return SNP ID and gene ID [Default = TRUE (if false returns only SNP ID with SNP location)]

Value

A dataframe with the following components:

SNP_ID NCBI dbSNP rs# cluster ID
Gene_ID NCBI gene ID (only if geneid.keep = TRUE)
Location SNP chromosomal base pair location (only if loc.keep = TRUE)

Author(s)

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

See Also

setSpecies getSNPs

Examples

## Not run: 
locs <- c(265772,33635700)
gene_ids <- c(530393)

# Returns SNP ID with gene ID and SNP location  for SNP locations - uses species set by setSpecies ()
snpids <- getSNPID (locs,id.type="loc")

# Returns SNP ID with gene ID for SNP locations - uses species set by setSpecies ()
snpids <- getSNPID (locs,id.type="loc",loc.keep=FALSE)

# Returns SNP ID with gene ID and SNP location if SNP is on the gene ID entered - uses species set by setSpecies ()
snpids <- getSNPID (gene_ids)

# Returns SNP ID with gene ID if SNP is on the gene ID entered(Bos taurus species)
snpids <- getSNPID (gene_ids,speciesCode="bta",geneid.keep=FALSE)

# Returns ALL SNP IDs - uses species set by setSpecies ()
snpids <- getSNPID ()
## End(Not run)

[Package FunctSNP version 1.0-1 Index]