runLMEM {MOCHA}

Run Linear Mixed-Effects Modeling for continuous, non-zero inflated data

Description

runLMEM Runs linear mixed-effects modeling for continuous, non-zero inflated data using lmer

Usage

runLMEM(
  ExperimentObj,
  assayName,
  modelFormula,
  initialSampling = 5,
  verbose = FALSE,
  numCores = 2
)

Arguments

ExperimentObj

A SummarizedExperiment object generated from getSampleTileMatrix, chromVAR, or other. It is expected to contain only one assay, or only the first assay will be used for the model. Data should not be zero-inflated.

assayName

The name of the assay to model within the SummarizedExperiment.

modelFormula

The formula to use with lmerTest::lmer, in the format (exp ~ factors). All factors must be found in column names of the ExperimentObj metadata. modelFormula must start with 'exp' as the response. See lmer.

initialSampling

Size of data to use for pilot

verbose

Set TRUE to display additional messages. Default is FALSE.

numCores

integer. Number of cores to parallelize across.

Value

results a SummarizedExperiment containing LMEM results. Assays are metrics related to the model coefficients, including the Estimate, Std_Error, df, t_value, p_value. Within each assay, each row corresponds to each row of the SummarizedExperiment and columns correspond to each fixed effect variable within the model. Any row metadata from the ExperimentObject (see rowData(ExperimentObj)) is preserved in the output. The Residual matrix and the variance of the random effects are saved in the metadata slot of the output.

Examples

## Not run: 
modelList <- runLMEM(ExperimentObj,
  assayName = names(ExperimentObj)[[1]]
  modelFormula = NULL,
  initialSampling = 5,
  verbose = FALSE,
  numCores = 1
)

## End(Not run)