Package index • bascule

Perform inference

Functions to fit NMF and clustering.

fit(): Fit a bascule object

fit_clustering(): Fit clustering

refine_denovo_signatures(): De novo signatures refinement.

merge_clusters(): Function to merge similar clusters

Getters

Utility functions to extract attributes.

get_input(): Get input data

get_signames(): Get signatures names

get_fixed_signames(): Get reference signatures names

get_denovo_signames(): Get denovo signatures names

get_signatures(): Get signatures

get_fixed_signatures(): Get fixed (reference) signatures

get_denovo_signatures(): Get de novo (reference) signatures

get_exposure(): Get exposures

get_n_denovo(): Get number of de novo signatures

get_n_groups(): Get number of groups

convert_dn_names(): Function to map de novo signatures to input catalogues

Plotting functions

Plotting functions available in the package

plot_data(): Function to visualize the input and reconstructed mutation counts.

plot_signatures(): Function to visualize the estimated and reference signatures.

plot_exposures(): Function to visualize the estimated exposures

plot_centroids(): Plot clustering centroids

plot_fit(): Report of the fit

plot_similarity_reference(): Function to visualize the similarity of denovo and reference signatures.

plot_scores(): Plot model selection scores

plot_gradient_norms(): Plot parameters gradients norms

plot_posterior_probs(): Plot posterior probabilities

S3 objects

Print and plot S3 functions

print(<bascule_obj>): Print for class 'bascule_obj'.

plot(<bascule_obj>): Plot for class 'bascule_obj'.

Data

Description of datasets available in the package.

COSMIC_sbs: COSMIC catalogue for SBS (version 3.4, GRCh37)

COSMIC_sbs_filt: COSMIC catalogue for SBS filtered (version 3.4, GRCh37)

COSMIC_dbs: COSMIC catalogue for DBS (version 3.4, GRCh37)

COSMIC_indels: COSMIC catalogue for Indels (version 3.4, GRCh37)

COSMIC_cn: COSMIC catalogue for CN (version 3.4, GRCh37)

Degasperi_SBS: Degasperi SBS catalogue

Degasperi_DBS: Degasperi DBS catalogue

synthetic_data: Analysis of a synthetic cohort

breast_data: Analysis of breast tumours

skin_metadata: Skin cohort metadata

skin_fit: Skin cohort BASCULE fit

Configure conda environment

Helper functions to create and check dependencies.

configure_environment(): Configure the reticulate environment

have_loaded_env(): Check if there is a loaded conda environment.

have_python_deps(): Check if Python packages are installed in the environment.

load_conda_env(): Load the input conda environment.

which_conda_env(): Retrieve the name of the currently loaded environment.