miniACC | R Documentation |
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).
data("miniACC")
A MultiAssayExperiment
with 5 experiments, providing:
RNA-seq count data: an ExpressionSet
with 198 rows and 79 columns
Reccurent copy number lesions identified by GISTIC2:
a SummarizedExperiment
with 198 rows and 90 columns
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"]])
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.
microRNA sequencing: an ExpressionSet
with
471 rows and 80 columns. Rows not having at least 5 counts in at least
5 samples were removed.
Levi Waldron lwaldron.research@gmail.com
https://github.com/waldronlab/multiassayexperiment-tcga
Zheng S et al.: Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell 2016, 29:723-736.
data("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")
)
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