miniACC {MultiAssayExperiment} | R Documentation

## Adrenocortical Carcinoma (ACC) MultiAssayExperiment

### Description

A `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 `colData(miniACC)`, and some additional details are provided by metadata(miniACC).

### Usage

    miniACC

### Format

A `MultiAssayExperiment` with 5 experiments, providing:

RNASeq2GeneNorm

  RNA-seq count data: an `ExpressionSet` with 198 rows and 79 columns

gistict

  Reccurent copy number lesions identified by GISTIC2: a `SummarizedExperiment` with 198 rows and 90 columns

RPPAArray

  Reverse Phase Protein Array: an `ExpressionSet` with 33 rows and 46 columns. Rows are indexed by genes, but protein annotations are available from `featureData(miniACC[["RPPAArray"]])`. The source of these annotations is noted in `abstract(miniACC[["RPPAArray"]])`

Mutations

  Somatic mutations: a `matrix` with 223 rows and 90 columns. 1 for any kind of non-silent mutation, zero for silent (synonymous) or no mutation.

miRNASeqGene

  microRNA sequencing: an `ExpressionSet` with 471 rows and 80 columns. Rows not having at least 5 counts in at least 5 samples were removed.

### Author(s)

Levi Waldron lwaldron.research@gmail.com

### Source

https://github.com/waldronlab/multiassayexperiment-tcga

### References

Zheng S *et al.*: Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell 2016, 29:723-736.

### 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")
    )

[Package MultiAssayExperiment version 1.20.0 Index]