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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
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

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.