\name{GeneAlterMB}
\docType{data}
\alias{GeneAlterMB}

\title{Data from the Parsons et al. 2011 study: Alterations for
  every gene and sample}
\description{Somatic alterations for each gene and tumor sample from the
  Parsons et al. 2011 medulloblastoma (MB) study.}

\usage{data(ParsonsMB11)}
\format{
  The somatic mutations in the MB study from Parsons et al., broken
  down by \emph{gene}, \emph{type} (point mutation, amplification,
  or deletion), \emph{sample},
  \emph{screen} (Discovery or Prevalence),
  and, for point mutations, \emph{mutation type},
  composed of the wild type nucleotide, its context,
  and the mutated nucleotide. The object is a data frame,
  with the variables: Gene, Type, Sample, Screen, WTNuc
  (wild type nucleotide), Context, and MutNuc (mutated
  nucleotide). The two possible values
  for Screen are Disc ("Discovery") and Prev ("Prevalence").
  The three possible values for Type are Mut (point mutations),
  Amp (large amplifications), and Del (large deletions.)
  Indels have a "" entry for WTNuc, an "All"
  entry for Context, and a "ins.del" entry for MutNuc.
  Large amplifications and deletions have "" entries for
  WTNuc, Context, and MutNuc.
}

\references{
  Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin J, Boca SM, Carter
  H, Samayoa J, Bettegowda C, et al.
  The genetic landscape of the childhood cancer medulloblastoma.
  \emph{Science.} DOI: 10.1126/science.1198056
  
  Parmigiani G, Lin J, Boca S, Sjoeblom T, Kinzler KW,
  Velculescu VE, Vogelstein B. Statistical methods for the analysis of
  cancer genome sequencing data. 
  \url{http://www.bepress.com/jhubiostat/paper126/}
}
\seealso{
  \code{cma.scores}, \code{cma.fdr},
  \code{cma.set.stat}, \code{cma.set.sim},
  \code{SimMethodsSims-class},
  \code{GeneCovMB}, 
  \code{GeneSampMB}
}

\keyword{datasets}