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.
This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see SNPlocs.Hsapiens.dbSNP142.GRCh37.
SNP locations for Homo sapiens (dbSNP Build 142)
Bioconductor version: 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>
citation("SNPlocs.Hsapiens.dbSNP142.GRCh37")):
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
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | Biostrings, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked(>= 1.3.19) |
| Linking To | |
| Enhances | |
| 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.dbSNP142.GRCh37_0.99.6.tar.gz |
| Windows Binary | |
| macOS Binary (x86_64) | |
| Package Short Url | https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP142.GRCh37/ |
| Package Downloads Report | Download Stats |