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To install this package, start R and enter:
## try http if https is not available
source("https://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: 3.1
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:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("SNPlocs.Hsapiens.dbSNP.20120608")
Documentation
| Reference Manual |
Details
| biocViews | AnnotationData, Genetics, Homo_sapiens |
| Version | 0.99.10 |
| 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 | 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_0.99.10.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.20120608/ |
| Package Downloads Report | Download Stats |
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