Integrative Inference of De Novo Cis-Regulatory Modules

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Documentation for package ‘BICORN’ version 0.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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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