pilotZIGLMM {MOCHA}

Execute a pilot run of 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 zero inflated data using glmmTMB. TryCatch will catch errors, and return the error and dataframe for troubleshooting.

Usage

pilotZIGLMM(
  TSAM_Object,
  cellPopulation = NULL,
  continuousFormula = NULL,
  ziformula = NULL,
  zi_threshold = 0,
  verbose = FALSE,
  pilotIndices = 1:10
)

Arguments

TSAM_Object

A SummarizedExperiment object generated from getSampleTileMatrix, chromVAR, or other.

cellPopulation

A single cell population on which to run this pilot model

continuousFormula

The formula, see glmmTMB. Combined fixed and random effects formula, following lme4 syntax.

ziformula

The zero-inflated formula, see glmmTMB. a one-sided (i.e., no response variable) formula for zero-inflation combining fixed and random effects: the default ~0 specifies no zero-inflation. Specifying ~. sets the zero-inflation formula identical to the right-hand side of formula (i.e., the conditional effects formula); terms can also be added or subtracted. When using ~. as the zero-inflation formula in models where the conditional effects formula contains an offset term, the offset term will automatically be dropped. The zero-inflation model uses a logit link.

zi_threshold

Zero-inflated threshold (range = 0-1), representing the fraction of samples with zeros. When the percentage of zeros in the tile is between 0 and zi_threshold, samples with zeroes are dropped and only the continous formula is used. Use this parameter at your own risk. Default is 0.

verbose

Set TRUE to display additional messages. Default is FALSE.

pilotIndices

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

Value

modelList a list of outputs from glmmTMB::glmmTMB