pilotLMEM {MOCHA}

Execute a pilot run of single linear model on a subset of data

Description

'r lifecycle::badge("deprecated")' This function is deprecated - improved modeling functions can be found in the package "ChAI" at https://github.com/aifimmunology/ChAI pilotLMEM Runs linear mixed-effects modeling for continuous, non-zero inflated data using lmer

Usage

pilotLMEM(
  ExperimentObj,
  assayName,
  modelFormula,
  pilotIndices = 1:10,
  verbose = FALSE
)

Arguments

ExperimentObj

A SummarizedExperiment-type object generated from chromVAR, makePseudobulkRNA, or other. Objects from getSampleTileMatrix can work, but we recommend runZIGLMM for those objects, not runLMEM>

assayName

a character string, matching the name of an assay within the SummarizedExperiment. The assay named will be used for modeling.

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.

pilotIndices

A vector of integers defining the subset of the ExperimentObj matrix. Default is 1:10.

verbose

Set TRUE to display additional messages. Default is FALSE.

Value

modelList a list of outputs from lmerTest::lmer