getCovariates {MOFA} | R Documentation

## getCovariates

### Description

This function extracts covariates from the `colData` in the input `MultiAssayExperiment` object.
Note that if you did not use `MultiAssayExperiment` to create your `createMOFAobject`, this function will not work.

### Usage

    getCovariates(object, covariate)

### Arguments

`object` | a `MOFAmodel` object.
`covariate` | names of the covariate

### Value

a vector containing the covariate

### Examples

    # Example on the CLL data
    library(MultiAssayExperiment)
    data("CLL_data", package = "MOFAdata")
    data("CLL_covariates", package = "MOFAdata")
    # Create MultiAssayExperiment object
    mae_CLL <- MultiAssayExperiment(CLL_data, colData=CLL_covariates)
    MOFAobject  <- createMOFAobject(mae_CLL)
    # Extract covariates from the colData of a MultiAssayExperiment
    gender <- getCovariates(MOFAobject, "Gender")
    diagnosis <- getCovariates(MOFAobject, "Diagnosis")
    # Example on the scMT data
    data("scMT_data", package = "MOFAdata")
    MOFAobject  <- createMOFAobject(scMT_data)
    # Extract covariates from the colData of a MultiAssayExperiment
    culture <- getCovariates(MOFAobject, "culture")
    # Extract covariates from the phenoData of the RNA assay
    cdr <- getCovariates(MOFAobject, "cellular_detection_rate")

[Package MOFA version 1.6.2 Index]