To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SNPlocs.Hsapiens.dbSNP.20110815")

In most cases, you don't need to download the package archive at all.

SNPlocs.Hsapiens.dbSNP.20110815

   

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see SNPlocs.Hsapiens.dbSNP.20110815.

SNP locations for Homo sapiens (dbSNP Build 134)

Bioconductor version: 3.1

SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 134. The source data files used for this package were created by NCBI on Aug 15, 2011, and contain SNPs mapped to reference genome GRCh37.p2. WARNING: Note that the GRCh37.p2 genome is a patched version of GRCh37 but the patch doesn't alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct location but this injection will exclude chrM (i.e. nothing will be injected in that sequence).

Author: Herve Pages

Maintainer: H. Pages <hpages at fhcrc.org>

Citation (from within R, enter citation("SNPlocs.Hsapiens.dbSNP.20110815")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SNPlocs.Hsapiens.dbSNP.20110815")

Documentation

PDF   Reference Manual

Details

biocViews AnnotationData, Genetics, Homo_sapiens
Version 0.99.7
License Artistic-2.0
Depends R (>= 2.10), IRanges, GenomicRanges
Imports methods, S4Vectors, IRanges, GenomicRanges
LinkingTo
Suggests Biostrings, BSgenome(>= 1.16.1), BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me VariantAnnotation

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source SNPlocs.Hsapiens.dbSNP.20110815_0.99.7.tar.gz
Windows Binary
Mac OS X 10.6 (Snow Leopard)
Mac OS X 10.9 (Mavericks)
Package Short Url http://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP.20110815/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center