SNPlocs.Hsapiens.dbSNP.20100427 {SNPlocs.Hsapiens.dbSNP.20100427} | R Documentation |
This package contains SNP locations and alleles for Homo sapiens extracted from dbSNP BUILD 131.
SNPs from dbSNP were filtered to keep only those satisfying the 3 following criteria:
The SNP is a single-base substitution i.e. its type is "snp". Other types used by dbSNP are: "in-del", "mixed", "microsatellite", "named-locus", "multinucleotide-polymorphism", etc... All those SNPs were dropped.
The SNP is marked as notwithdrawn.
A single location on the reference genome (GRCh37) is reported for the SNP.
The source data files used for this package were created by NCBI on 24-26 March 2010.
WARNING: The SNPs in this package are based on the GRCh37 genome. Note that the GRCh37 genome 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 but this injection will exclude chrM (i.e. nothing will be injected in that sequence).
See http://www.ncbi.nlm.nih.gov/snp, the SNP Home at NCBI, for more information about dbSNP.
See ?injectSNPs
in the BSgenome software
package for more information about the SNP injection mechanism.
See http://genome.ucsc.edu/cgi-bin/hgGateway?clade=mammal&org=Human&db=hg19 for more information about the Human Feb. 2009 (GRCh37/hg19) assembly used by the UCSC Genome Browser.
H. Pages
SNP Home at NCBI: http://www.ncbi.nlm.nih.gov/snp
dbSNP Build 131:human_9606 announcement: http://www.ncbi.nlm.nih.gov/mailman/pipermail/dbsnp-announce/2010q1/000094.html
About the Human Feb. 2009 (GRCh37/hg19) assembly used by the UCSC Genome Browser: http://genome.ucsc.edu/cgi-bin/hgGateway?clade=mammal&org=Human&db=hg19
getSNPlocs
for how to access the data stored in this package.
injectSNPs
in the BSgenome package for more
information about SNP injection.