snpLocs.Hs {GGBase}R Documentation

SNP location accessor

Description

SNP location accessor

Usage

snpLocs.Hs(cnum, rsid)

Arguments

cnum chrnum instance indicating chromosome
rsid rsid instance giving dbSNP ids for snps of interest

Details

The SNPlocs.Hsapiens.dbSNP.* package is curated by Bioconductor and maintains location and allele information on SNP.

The hsSnpLocs environment is available through data(hsSnpLocs), and contains a unified representation of the information in the SNPlocs package (which is only available through various chromosome-specific calls).

Value

two-row matrix – top row is numeric suffix of dbSNP ids, bottom row is location, genome-wide if chrnum is missing

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

Examples

library(GGtools)
data(hmceuB36.2021)
nn21 = colnames(smList(hmceuB36.2021)[["21"]])
length(nn21)
ss = snpLocs.Hs(chrnum(21), rsid(nn21))
dim(ss)
# notes that the locations available are not completely
# congruent with those asserted in HapMap data

[Package GGBase version 3.4.0 Index]