SNPlocs.Hsapiens.dbSNP142.GRCh37

DOI: 10.18129/B9.bioc.SNPlocs.Hsapiens.dbSNP142.GRCh37    

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

SNP locations for Homo sapiens (dbSNP Build 142)

Bioconductor version: Release (3.15)

SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 142. The source data files used for this package were created by NCBI on October 14, 2014, and contain SNPs mapped to reference genome GRCh37.p13. WARNING: Note that the GRCh37.p13 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: Simon Coetzee

Maintainer: Simon Coetzee <simon.coetzee at cshs.org>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("SNPlocs.Hsapiens.dbSNP142.GRCh37")

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

Documentation

PDF		Reference Manual

Details

biocViews	AnnotationData, Genetics, Homo_sapiens, SNPlocs
Version	0.99.6
License	Artistic-2.0
Depends	R (>= 2.10), IRanges, GenomeInfoDb, GenomicRanges, BSgenome(>= 1.25.6)
Imports	methods, utils, IRanges, GenomeInfoDb, GenomicRanges, BSgenome
LinkingTo
Suggests	Biostrings, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked(>= 1.3.19)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	motifbreakR
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Package Archives

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

Source Package	SNPlocs.Hsapiens.dbSNP142.GRCh37_0.99.6.tar.gz
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Package Short Url	https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP142.GRCh37/
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