dot-retrieve_covariates: Retrieve the covariates from a SCE colData

In combiz/scFlow: A Single-Cell/Nuclei Analysis Toolkit

Retrieve the covariates from a SCE colData

Description

Retrieve the covariates from a SCE colData

Usage

.retrieve_covariates(
  sce,
  unique_id_var,
  dependent_var,
  confounding_vars,
  ref_class,
  ...
)

Arguments

sce	a SingleCellExperiment object
unique_id_var	the unique identifier variable for each sample
dependent_var	the name of the colData variable for contrasts
ref_class	the class of dependent_var used as reference

Value

mat a dataframe with covariates ordered by unique_id_var

See Also

Other helper: .append_cell_metric_plots_sce(), .append_cell_prop_plots_sce(), .clean_ggplot_plot_env(), .clean_ggplot_quosures(), .clean_quosure_env(), .fancy_scientific(), .get_d_palette(), .grobify_ggplot(), .model_fisher_celltype(), .plot_dirichlet_results(), .plot_unique_id_var(), .prepare_dirichlet_plot_table(), .prepare_fisher_counts_table(), .prepare_unique_id_var_plot_table(), .process_dirichlet_fit(), .tally_cells(), .uniftest()

combiz/scFlow documentation built on Feb. 25, 2024, 10:25 a.m.