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]