The CeTF Class

The CeTF class is data storage class that stores all the results from runAnalysis function.

Value

Returns an CeTF object.

Slots

Data

Includes the raw, tpm and norm (see normExp) data.

DE

Includes the uniquely differentially expressed genes/TFs and the statistics for all genes (see expDiff).

Input

Includes input matrices for RIF (see RIF) and PCIT (see PCIT) for both conditions in runAnalysis function analysis.

Output

Includes the matrix output from RIF analysis (see RIF) and a matrix with PCIT output, and other two matrix with raw and significant adjacency (see PCIT) for both conditions inside of runAnalysis function analysis.

Network

Network with Gene-Gene and Gene-TF interactions for both conditions (see PCIT), main TFs resulted from the complete analysis, all the TFs identified in the input data and matrix annotating all genes and TFs.