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

pcawg_priors: Priors from PCAWG

cancer_gene_census: Gene roles from COSMIC Cancer Gene Census

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

INCOMMON classification

Main functions to classify mutations

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

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

Visualisation

Functions to plot INCOMMON classification results

plot_classification(): Visualize classification results for individual observations.

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

plot_class_fraction(): Visualize frequency distribution of INCOMMON classes.

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

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

classification(): Getter for class 'INCOMMON'.

parameters(): Getter for class 'INCOMMON'.

priors(): Getter for class 'INCOMMON'.

posterior(): Getter for class 'INCOMMON'.

INCOMMON Model

Functions to compute model likelihood and posterior distributions

compute_likelihood(): Compute model likelihood

compute_posterior(): Compute model posterior and entropy

genome_interpreter(): This function returns, for each mutation, an interpreted state depending on the mutant gene role and its copy-number and multiplicity, among Mutant TSG with or without LOH, and Mutant oncogene with or without amplification. In addition, it assigns an interpreted genome to each sample by integrating the interpreted state of each mutant gene in the sample.

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.