SNPlocs.Hsapiens.dbSNP.20100427 {SNPlocs.Hsapiens.dbSNP.20100427}R Documentation

The SNPlocs.Hsapiens.dbSNP.20100427 package

Description

This package contains SNP locations and alleles for Homo sapiens extracted from dbSNP BUILD 131.

Details

SNPs from dbSNP were filtered to keep only those satisfying the 3 following criteria:

Note

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.

Author(s)

H. Pages

References

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

See Also

getSNPlocs for how to access the data stored in this package.

injectSNPs in the BSgenome package for more information about SNP injection.


[Package SNPlocs.Hsapiens.dbSNP.20100427 version 0.99.6 Index]