Reference

Available data Data released with the package.
multiome_congas_object	Multiome congas object
metadata	Dataframe containing cell type annotations for the 10x multiome lymphoma dataset.
atac_counts	Example tibbles with input ATAC data in the format for (R)CONGAS+
rna_counts	Example tibbles with input RNA data in the format for (R)CONGAS+
Main functions Functions to create and fit a dataset.
create_congas_tibble()	Format the input counts before creating the CONGAS+ object
init()	Create a dataset.
auto_config_run()	Determine data-based hyperparameters for the Bayesian priors.
auto_normalisation_factor()	Compute empirical normalisation factors (library size)
segments_selector_congas()	Filter segments where the optimal number of clusters is 1.
fit_congas()	Fit an (R)CONGAS+ model
Getters Functions to extract information from a model.
get_input()	Extract input data.
get_fit()	Extract fit data.
stat()	Compute the statistics of a dataset.
Filtering Functions to pre-process inputs and post-process models.
filter_known_genes()	Filter genes from an RNA tibble.
filter_counts_by_quantile()	Filter observed counts by quantile.
filter_segments()	Filter segments.
filter_outliers()	Filter per-segment outliers by quantiles.
filter_missing_data()	Filter per-segment outliers by quantiles.
Plotting functions Functions to plot data and fits.
plot_data()	Plot data.
plot_fit()	Plot fits.
S3 functions The rcongasplus S3 object functions.
print.rcongasplus()	Print for an object of class 'rcongasplus'.
plot(<rcongasplus>)	Plot for an object of class 'rcongasplus'.
Downstream analyses Functions to perform additional analyses downstream of the CONGAS+ inference.
build_clone_tree()	Build Clone Tree form a CONGAS+ object Using medicc2