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CIE: Causal Inference Engine: Directional Enrichment Analysis on Biological Networks

Introduction

This page provides the instructions for running active regulator inference analysis using the CIE R-package. CIE includes many options for running inference, processing networks and visualizations. To see these options run ?runCIE from the R console in which CIE library is loaded.

Table of Contents

Input Requirements

Graphing Legend

Additional Information

Input Requirements

Users must provide the following required inputs:

1. DGEs table: A data frame containing differential gene expression data with at least the following three case-insensitive named columns.
   • Entrez id as: id, entr, or Entrez
   • p-value as: qval, q.val, q-val, q-val, P-value, P.value, pvalue, pval, or Pval
   • Fold Change as: FC, fold, FoldChange
2. databaseType and databaseDir, corresponding to the name and files for one of our supported networks, or ents and rels data frames.
3. Inference method: one of Fisher, Ternary, or Quaternary.

Graphing Legend

The package we use to display graphs does not allow legends. For your convenience, the legend is shown below.

Graphing Legend

Additional Information

Custom Networks

Information on what is required of a network for this package. Helpful if you wish to customize the networks available.

Example Analysis

An example analysis using one of the sample inputs available through our app.