Package index • INCOMMON

Available data

Datasets included in the package.

MSK_genomic_data: Genomic data of the MSK-MetTropism cohort

MSK_clinical_data: Genomic data of the MSK-MetTropism cohort

priors_pcawg_hmf: Priors over (k,m) configurations from PCAWG and HMF

priors_eta: Priors over the rate of reads per chromosome copy from MSK-MET

cancer_gene_census: Gene roles from COSMIC Cancer Gene Census

MSK_PAAD_output: Data from the MSK-MetTropism cohort classified with INCOMMON

INCOMMON classification

Main functions to classify mutations

compute_eta_prior(): Evaluate a prior distribution over the rate of reads per chromosom copy from the data.

priors_k_m(): Getter for class 'INCOMMON'.

subset_sample(): Subset an INCOMMON object by sample ID.

init(): Prepare input for analyses with 'INCOMMON'.

classify(): Classify mutations using a Beta-Binomial model-based test.

Visualisation

Functions to plot INCOMMON classification results

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

plot_prior(): Visualize prior distribution for a gene (tumor-specific or pancancer).

plot_eta_prior(): Visualise the prior distribution over the rate of reads per chromosome copy.

plot_purity_prior(): Visualise the prior distribution on sample purity

plot_posterior_k_m(): Visualise the posterior distribution on (k,m) configurations.

plot_class_fraction(): Visualize frequency distribution of INCOMMON classes.

plot_survival_analysis(): Visualise survival analysis based on INCOMMON classes.

plot_met_volcano(): Visualize metastatic propnesity odds ratio in a volcano plot fashion.

plot_tropism(): Visualize metastatic propnesity odds ratio in a volcano plot fashion.

Getter Functions

Functions to extract model information

parameters(): Getter for class 'INCOMMON'.

show_FAM(): Get the fraction of alleles with the mutation (FAM) values for a gene and cancer type.

posterior_k_m(): Get the posterior distribution over (k,m) configurations for a specific mutation

INCOMMON Model

Functions to compute model likelihood and posterior distributions

mutant_dosage_classification(): Group patients by gene mutant mutant dosage using gene-role specific thresholds.

compute_expectations(): Compute the expectation value of k, m and FAM from the model full posterior distribution.

Survival analysis with INCOMMON classes

Functions to perform survival analysis with patient stratificaiton based on INCOMMON classes

kaplan_meier_fit(): Fit Kaplan-Meier survival model stratifying patients based on INCOMMON classes, for a single gene and tumour type.

cox_fit(): Fit multivariate Cox regression model based on INCOMMON classes.

plot_survival_analysis(): Visualise survival analysis based on INCOMMON classes.

Metastatic pattern analysis with INCOMMON classes

Functions to perform metastatic propensity and tropism analysis with INCOMMON interpreted tumor genomes

met_propensity(): Logistic regression of metastatic propensity based on INCOMMON classes.

met_tropism(): Logistic regression of metastatic tropism based on INCOMMON classes.