Summary of the MultiAssayExperiment API

Updated from Ramos et al., Cancer Research 2017; DOI: 10.1158/0008-5472.CAN-17-0344

API Overview

Constructors

Function Description Returned Class
MultiAssayExperiment Create a MultiAssayExperiment object MultiAssayExperiment
ExperimentList Create an ExperimentList from a List or list ExperimentList

Accessors

Function Description Returned Class
colData Get or set data that describe patients / biological units DataFrame
experiments Get or set the list of experimental data objects ExperimentList
assays Get the list of experimental numeric matrices SimpleList
assay Get the first experimental numeric matrix matrix, matrix-like
sampleMap Get or set the map relating observations to subjects DataFrame
metadata Get or set additional data descriptions list
rownames Get row names for all experiments CharacterList
colnames Get column names for all experiments CharacterList
getWithColData Extract a single assay with whole or assay colData (varies)

Subsetting

Syntax Description Returned Class
mae[i, j, k] Get rows, columns, and/or experiments MultiAssayExperiment
mae[i,,] – i: GRanges, character, integer, etc. MultiAssayExperiment
mae[,j,] – j: character, integer, logical, etc. MultiAssayExperiment
mae[,,k] – k: character, integer, logical MultiAssayExperiment
mae[[n]] Get/set object from experiments (varies)
mae$column Get/set colData column vector (varies)
getWithColData(mae, k) Extract a single assay with colData; k: char, int (varies)
subsetByColData(mae, ..) Select rows from colData and re-harmonize data MultiAssayExperiment

Management

Function Description Returned Class
prepMultiAssay Troubleshoot constructor problems constructing class list
complete.cases Identify subjects with complete data logical vector
replicated Identify replicate observations per experiment list of LogicalLists
anyReplicated Whether any replicate observations exist logical vector
showReplicated Show actual technical replicate obs. in assay list of CharacterLists
mergeReplicates Merge replicate observations within each experiment MultiAssayExperiment
intersectRows Features present in all experiments MultiAssayExperiment
intersectColumns Subjects with data in all experiments MultiAssayExperiment
renameColname Rename the assay column names for a single assay MultiAssayExperiment
renamePrimary Rename the colData rownames MultiAssayExperiment
splitAssay Separate columns from assays using a ‘hitList’ of logical vectors MultiAssayExperiment
makeHitList Create a ‘hitList’ list based on patterns for matching assay colnames list

Reshaping

Function Description Returned Class
longFormat Long tidy DataFrame with optional colData columns DataFrame
wideFormat Wide format, one row per subject DataFrame

Combining

Function Description Returned Class
c Concatenate experiment to MAE MultiAssayExperiment

Coercion

Function Description Returned Class
MultiAssayExperimentToMAF Convert MAE to MAF using ‘non_syn’ and ‘syn’ assays maftools::MAF

Export

Function Description Returned Class
exportClass Save all data from a MAE to a series of text files (‘.csv’) (files)
saveHDF5MultiAssayExperiment Save a MAE in ‘.h5’ and ‘.rds’ formats similar to HDF5Array::saveHDF5SummarizedExperiment (files)

Notes

  • assay: Procedure for measuring biological activity (e.g., RNA-seq).
  • experiment: Application of an assay to a sample set.
  • mae: A MultiAssayExperiment object.
  • subject: Patient, cell line, or other biological unit.
  • observation: Results of an assay (e.g., gene expression).
  • features: Measurement units labeled by row names or genomic ranges.
  • duplicated() was deprecated in Bioconductor 3.7 and replaced by replicated().