Take a MultiAssayExperiment and include curated variables

This function works on the colData of a MultiAssayExperiment object to merge curated variable columns or other clinical variables that would like to be added. It is recommended that the user run the scripts in the MultiAssayExperiment.TCGA repository that build the "enhanced" type of data but not necessary if using different clinical data. Please see the repository's README for more information.

Usage

mergeColData(MultiAssayExperiment, colData)

Arguments

MultiAssayExperiment

A MultiAssayExperiment object

colData

A DataFrame or data.frame to merge with clinical data in the MultiAssayExperiment object

Value

A MultiAssayExperiment object

Examples

library(MultiAssayExperiment)

mergeColData(MultiAssayExperiment(), S4Vectors::DataFrame())
#> A MultiAssayExperiment object of 0 listed
#>  experiments with no user-defined names and respective classes.
#>  Containing an ExperimentList class object of length 0:
#>  Functionality:
#>  experiments() - obtain the ExperimentList instance
#>  colData() - the primary/phenotype DataFrame
#>  sampleMap() - the sample coordination DataFrame
#>  `$`, `[`, `[[` - extract colData columns, subset, or experiment
#>  *Format() - convert into a long or wide DataFrame
#>  assays() - convert ExperimentList to a SimpleList of matrices
#>  exportClass() - save data to flat files