\name{MafDb.ExAC.r0.3.sites-package}
\alias{MafDb.ExAC.r0.3.sites-package}
\alias{MafDb.ExAC.r0.3.sites}
\docType{package}

\title{
Annotation package for minor allele frequency data from the Exome Aggregation Consortium
}
\description{
This annotation package stores minor allele frequency (MAF) data derived from the variant set release 0.3 of the Exome Aggregation Consortium. The data is stored in the form of a SQLite database and is loaded automatically in the form of a MafDb object. The name of the exposed object matches the name of the package and part of the filename that contained the data imported into the package. The class definition and methods to access MafDb objects are found in the \code{\link[VariantFiltering]{VariantFiltering}} software package.

Please consult the ExAC FAQ page at \url{http://exac.broadinstitute.org/faq} before you use these data for your own research.
}

\format{
  \tabular{ll}{
    \code{\link{MafDb.ExAC.r0.3.sites-package}} \tab MafDb object containing MAF values from the Exome Aggregation Consortium downloaded in October 2015 from \url{ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3/ExAC.r0.3.sites.vep.vcf.gz}. See \code{\link{makeMafDbPackageExAC}} for more information on how to update these data. \cr
  }
}

\author{
R. Castelo
}

\seealso{
  \link{makeMafDbPackageExAC}
  \link[MafDb.ALL.wgs.phase1.release.v3.20101123]{MafDb.ALL.wgs.phase1.release.v3.20101123}
  \link[MafDb.ALL.wgs.phase3.release.v5a.20130502]{MafDb.ALL.wgs.phase3.release.v5a.20130502}
  \link[MafDb.ESP6500SI.V2.SSA137]{MafDb.ESP6500SI.V2.SSA137}
  \link[VariantFiltering]{MafDb-class}
  \link[VariantFiltering]{snpid2maf}
  \link[VariantFiltering]{VariantFiltering}
}

\examples{
library(MafDb.ExAC.r0.3.sites)

ls("package:MafDb.ExAC.r0.3.sites")

mafdb <- MafDb.ExAC.r0.3.sites
mafdb

knownVariantsMAFcols(mafdb)

## lookup allele frequencies for rs1129038, a SNP associated to blue and brown eye colors
## as reported by Eiberg et al. Blue eye color in humans may be caused by a perfectly associated
## founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression.
## Human Genetics, 123(2):177-87, 2008 [http://www.ncbi.nlm.nih.gov/pubmed/18172690]
snpid2maf(mafdb, "rs1129038")
}

\source{
  The Exome Aggregation Consortium (ExAC), Cambridge, MA
  (URL: \url{http://exac.broadinstitute.org}) [October, 2015, accessed]
}

\keyword{package}
\keyword{data}