File: miniACC.Rd

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r-bioc-multiassayexperiment 1.16.0%2Bdfsg-1
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{miniACC}
\alias{miniACC}
\title{Adrenocortical Carcinoma (ACC) MultiAssayExperiment}
\format{
A \code{MultiAssayExperiment} with 5 experiments, providing:
\describe{
    \item{RNASeq2GeneNorm}{RNA-seq count data: an \code{ExpressionSet}
    with 198 rows and 79 columns}
    \item{gistict}{Reccurent copy number lesions identified by GISTIC2:
    a \code{SummarizedExperiment} with 198 rows and 90 columns}
    \item{RPPAArray}{Reverse Phase Protein Array: an \code{ExpressionSet}
    with 33 rows and 46 columns. Rows are indexed by genes,
    but protein annotations are available from
    \code{featureData(miniACC[["RPPAArray"]])}. The source of these
    annotations is noted in \code{abstract(miniACC[["RPPAArray"]])}}
    \item{Mutations}{Somatic mutations: a \code{matrix} with 223 rows and
    90 columns. 1 for any kind of non-silent mutation, zero for silent
    (synonymous) or no mutation.}
    \item{miRNASeqGene}{microRNA sequencing: an \code{ExpressionSet} with
    471 rows and 80 columns. Rows not having at least 5 counts in at least
    5 samples were removed.}
}
}
\source{
https://github.com/waldronlab/multiassayexperiment-tcga
}
\usage{
miniACC
}
\description{
A \code{\link{MultiAssayExperiment}} object providing a reduced version of
the TCGA ACC dataset for all 92 patients. RNA-seq, copy number, and somatic
mutations are included only for genes whose proteins are included in the
reverse-phase protein array. The MicroRNA-seq dataset is also included,
with infrequently expressed microRNA removed. Clinical, pathological, and
subtype information are provided by \code{colData(miniACC)}, and some
additional details are provided by metadata(miniACC).
}
\examples{

miniACC
metadata(miniACC)
colnames(colData(miniACC))
table(miniACC$vital_status)
longFormat(
    miniACC["MAPK3", , ],
    colDataCols = c("vital_status", "days_to_death")
)

wideFormat(
    miniACC["MAPK3", , ],
    colDataCols = c("vital_status", "days_to_death")
)

}
\references{
Zheng S *et al.*: Comprehensive Pan-Genomic Characterization of
Adrenocortical Carcinoma. Cancer Cell 2016, 29:723-736.
}
\author{
Levi Waldron \email{lwaldron.research@gmail.com}
}
\keyword{data}