`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.