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

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Documentation for package ‘HiCPotts’ version 0.99.5

• 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