getCovariates {MOFA} | R Documentation |
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.
getCovariates(object, covariate)
object |
a |
covariate |
names of the covariate |
a vector containing the covariate
# 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")