To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("SNPlocs.Hsapiens.dbSNP.20120608")

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

SNPlocs.Hsapiens.dbSNP.20120608

SNP locations for Homo sapiens (dbSNP Build 137)

Bioconductor version: Release (3.0)

SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 137. The source data files used for this package were created by NCBI on June 7-8, 2012, and contain SNPs mapped to reference genome GRCh37.p5. WARNING: Note that the GRCh37.p5 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.20120608")):

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("SNPlocs.Hsapiens.dbSNP.20120608")

Documentation

PDF   Reference Manual

Details

biocViews AnnotationData, Genetics, Homo_sapiens
Version 0.99.9
License Artistic-2.0
Depends R (>= 2.10), IRanges, GenomicRanges, BSgenome(>= 1.25.6)
Imports methods, utils, IRanges, GenomicRanges, BSgenome
Suggests Biostrings, BSgenome.Hsapiens.UCSC.hg19(>= 1.3.19)
System Requirements
URL
Depends On Me ggtut
Imports Me
Suggests Me AllelicImbalance, cheung2010, GGtools, VariantFiltering

Package Archives

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

Package Source SNPlocs.Hsapiens.dbSNP.20120608_0.99.9.tar.gz
Windows Binary SNPlocs.Hsapiens.dbSNP.20120608_0.99.9.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) SNPlocs.Hsapiens.dbSNP.20120608_0.99.9.tgz
Mac OS X 10.9 (Mavericks) SNPlocs.Hsapiens.dbSNP.20120608_0.99.9.tgz
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