# HiCPotts: Hierarchical Modeling to Identify and Correct Genomic Biases in Hi-C

## Documentation for package ‘HiCPotts’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

compute_HMRFHiC_probabilities | Compute HMRFHiC Probabilities of Assigning an Interaction to Each Component
gamma_prior_value | Prior Value for the Potts Model Interaction Parameter
get_data | Extract Hi-C Bin Interactions with GC, Accessibility, and TE Counts
likelihood_combined | Likelihood Function for a Specified Model Component and Distribution
likelihood_gamma | Likelihood Function for the Interaction Parameter in a Potts Model
posterior_combined | Compute the Posterior for the Model Components
pred_combined | Prediction Function for Combined Model
prior_combined | Prior Function for Model Components
process_data | CSV file Data Processing for Hi-C Interaction Matrices and Covariates
proposaldensity_combined | Proposal Density Function for Model Components
proposalfunction | Proposal Function for the Potts Model Interaction Parameter
pz_123 | Posterior Function for the Potts Model
run_chain_betas | MCMC Chain Execution for HiCPotts Simulations
run_metropolis_MCMC_betas | Run Metropolis-Hastings MCMC for HMRFHiC Model
size_prior | Size Prior for the Negative Binomial-Type Distributions