Function reference • basilica

Perform inference

Functions to fit NMF and clustering.

fit(): Fit a basilica object

fit_clustering(): Fit clustering

Getters

Utility functions to extract attributes.

get_input(): Get input data

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

merge_clusters(): Function to merge similar clusters

plot_fit(): Report of the fit

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

S3 objects

Print and plot S3 functions

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

plot(<basilica_obj>): Plot for class 'basilica_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_filt_merged: COSMIC catalogue (version XXXX)

Degasperi_SBS_GEL_PCAWG_HW: SBS data for PMID: 35949260

Degasperi_catalogue: Degasperi catalogue (version XXXX)

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.