miniACC: Adrenocortical Carcinoma (ACC) MultiAssayExperiment

In MultiAssayExperiment: Software for the integration of multi-omics experiments in Bioconductor

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 [e-mail]

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")
)

MultiAssayExperiment documentation built on Nov. 8, 2020, 8:10 p.m.