pilotZIGLMM: 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
)

Value

modelList a list of outputs from glmmTMB::glmmTMB

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.