SNPlocs.Hsapiens.dbSNP.20120608

DOI: 10.18129/B9.bioc.SNPlocs.Hsapiens.dbSNP.20120608    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see SNPlocs.Hsapiens.dbSNP.20120608.

SNP locations for Homo sapiens (dbSNP Build 137)

Bioconductor version: 3.9

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). IMPORTANT NOTE: This package is deprecated. Please use a SNPlocs data package based on a more recent dbSNP BUILD instead (e.g. BUILD 144 or BUILD 149). You can call BSgenome::available.SNPs() from R to get the list of available SNPlocs data packages.

Author: Herve Pages

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SNPlocs.Hsapiens.dbSNP.20120608")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	AnnotationData, Genetics, Homo_sapiens
Version	0.99.11
License	Artistic-2.0
Depends	R (>= 2.10), IRanges, GenomicRanges, BSgenome(>= 1.25.6)
Imports	methods, utils, IRanges, GenomicRanges, BSgenome
LinkingTo
Suggests	Biostrings, BSgenome.Hsapiens.UCSC.hg19(>= 1.3.19)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	motifbreakR
Links To Me

Package Archives

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

Source Package	SNPlocs.Hsapiens.dbSNP.20120608_0.99.11.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Package Short Url	https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP.20120608/
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