varZIGLMM {MOCHA}

Zero-inflated Variance Decomposition for pseudobulked scATAC 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 varZIGLMM Identified variance decomposition on a given cell type across both zero-inflated and continuous space using a zero-inflated general linear mixed model glmmTMB

Usage

varZIGLMM(
  TSAM_Object,
  cellPopulation = NULL,
  continuousRandom = NULL,
  ziRandom = NULL,
  zi_threshold = 0.1,
  verbose = FALSE,
  numCores = 1
)

Arguments

TSAM_Object

A SummarizedExperiment object generated from getSampleTileMatrix.

cellPopulation

Name of a cell type(s), or 'all'. The function will combine the cell types mentioned into one matrix before running the model.

continuousRandom

Random effects to test in the continuous portion. All factors must be found in column names of the TSAM_Object metadata, except for FragNumber and CellCount, which will be extracted from the TSAM_Object's metadata.

ziRandom

Random effects to test in the zero-inflated portion. All factors must be found in column names of the TSAM_Object colData metadata, except for FragNumber and CellCount, which will be extracted from the TSAM_Object's metadata.

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.

numCores

integer. Number of cores to parallelize across.

Value

results a SummarizedExperiment containing results from ZIGLMM (Fixed effect estiamtes, P-values, and Std Error)

Examples

## Not run: 
modelList <- runZIGLMM(STM[c(1:1000), ],
  cellPopulation = "CD16 Mono",
  continuousRandom = c("Age", "Sex", "Days"),
  ziRandom = c("FragNumber", "Days"),
  verbose = TRUE,
  numCores = 35
)

## End(Not run)