biomart.SNP.rsID: Fetches the rs SNP IDs given the chromosomal coordinates and...

In alesssia/timesaveR: Widely used function to save time on everyday work

Fetches the rs SNP IDs given the chromosomal coordinates and alleles

Description

Uses biomaRt function to fetch the rs SNP ID for the given chromosoma coordinates and alleles. If no SNP is found in that position with those alleles NA is returned. It uses the given BioMart database.

Usage

biomart.SNP.rsID(
  chr,
  ps,
  allele0,
  allele1,
  mart,
  with.position = FALSE,
  with.alleles = FALSE
)

Arguments

chr	chromosome number (1, 2, ...)
ps	position (bp)
allele0	alternate allele
allele1	reference allele
mart	BioMart database
with.position	whether including chromosome name and start and end position (default: false)
with.alleles	whether including variant alleles (default: false, if with.position==TRUE is forced to TRUE)

Value

reference SNP IDs, or reference SNP IDs plus genomic coordinates and alleles

Author(s)

Alessia Visconti, Niccolo' Rossi

Examples

mybiomart <- biomart.fetch.SNP.grch37.mart()
biomart.SNP.rsID(7, 24966446, "C", "A", mybiomart)
biomart.SNP.rsID(17, 75020291, "A", "G", mybiomart)
biomart.SNP.rsID(7, 24966446, "C", "A", mybiomart, with.position=TRUE)
biomart.SNP.rsID(17, 75020291, "A", "G", mybiomart, with.alleles=TRUE)
biomart.SNP.rsID(5, 70119760, "A", "G", mybiomart, with.alleles=TRUE)

alesssia/timesaveR documentation built on Jan. 26, 2024, 5:21 p.m.