Integrative Inference of De Novo Cis-Regulatory Modules

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Documentation for package ‘BICORN’ version 0.1.0

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A TF-gene regulation strength matrix
alpha Inverse-gamma distribution hyper-parameter alpha
A_old TF-gene regulation strength matrix sampled from the previous round
A_sampling Regulation Strength Sampling Function
baseline_sampling Gene Baseline Expression Sampling Function
base_line Gene baseline expression
base_line_old Gene baseline expression sampled from the previous round.
beta Inverse-gamma distribution hyper-parameter beta
BICORN BICORN Algorithm Function
Binding_genes Genes in the prior binding network
Binding_matrix Prior TF-gene binding network
Binding_TFs TFs in the prior binding network
C TF-gene binding network
C_old TF-gene binding network sampled from the previous round
C_prior Prior TF-gene binding network
C_sampling_cluster cis-Regulatory Module Sampling Function
data_integration Data Initialization for BICORN
Exp_data Gene expression data
Exp_genes Genes in the expression data
sigmanoise_sampling Fitting Residule Variance Sampling Function
sigma_A Regulation strength variance
sigma_baseline Variance of baseline gene expression.
sigma_noise Variance of gene expression fitting residuals.
sigma_X Transcription factor activity variance
X Transcription factr activity matrix
X_old Transcription factr activity matrix sampled from the previous round
X_sampling Transcription Factor Activity Sampling Function
Y Gene expression data used for module inference