fit_models: Fits a model for each gene in a cell_data_set object.

Description Usage Arguments Value

View source: R/expr_models.R

Description

This function fits a generalized linear model for each gene in a cell_data_set. Formulae can be provided to account for additional covariates (e.g. day collected, genotype of cells, media conditions, etc).

Usage

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fit_models(
  cds,
  model_formula_str,
  expression_family = "quasipoisson",
  reduction_method = "UMAP",
  cores = 1,
  clean_model = TRUE,
  verbose = FALSE,
  ...
)

Arguments

cds

The cell_data_set upon which to perform this operation.

model_formula_str

A formula string specifying the model to fit for the genes.

expression_family

Specifies the family function used for expression responses. Can be one of "quasipoisson", "negbinomial", "poisson", "binomial", "gaussian", "zipoisson", or "zinegbinomial". Default is "quasipoisson".

reduction_method

Which method to use with clusters() and partitions(). Default is "UMAP".

cores

The number of processor cores to use during fitting.

clean_model

Logical indicating whether to clean the model. Default is TRUE.

verbose

Logical indicating whether to emit progress messages.

...

Additional arguments passed to model fitting functions.

Value

a tibble where the rows are genes and columns are


cole-trapnell-lab/monocle3 documentation built on April 8, 2021, 5:54 a.m.