# Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

## Documentation for package ‘CeTF’ version 1.25.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

bivar.awk | Summary statistics from two variables
CeTF | The CeTF Class
CeTF-class | The CeTF Class
CeTFdemo | CeTFdemo class object example
CircosTargets | Circos plot for the Transcription Factors/genes targets.
clustCoef | Calculate the clustering coefficient
clustCoefPercentage | Calculate the clustering coefficient as a percentage
densityPlot | Density distribution of correlation coefficients and significant PCIT values
diffusion | Network diffusion analysis
enrichdemo | Enrichment data
enrichPlot | Plots to visualize the enrichment analysis results
expDiff | Differential expression analysis
getData | Data accessor for a CeTF class object.
getData-method | Data accessor for a CeTF class object.
getDE | Differential Expression accessor for a CeTF class object.
getDE-method | Differential Expression accessor for a CeTF class object.
getEnrich | Enrichment analysis for genes of network
getGroupGO | Functional Profile of a gene set at specific GO level
gtfToBed | Converts GTF to BED
heatPlot | Heatmap-like functional classification
histPlot | Histogram of connectivity distribution
InputData | Input data accessor for a CeTF class object.
InputData-method | Input data accessor for a CeTF class object.
netConditionsPlot | Network plot of gene-gene/gene-TFs interactions
netGOTFPlot | Plot a network for Ontologies, genes and TFs
NetworkData | Networks data accessor for a CeTF class object.
NetworkData-method | Networks data accessor for a CeTF class object.
normExp | Normalized expression transformation
OutputData | Output data accessor for a CeTF class object.
OutputData-method | Output data accessor for a CeTF class object.
PCIT | Partial Correlation and Information Theory (PCIT) analysis
pcitC | A helper to calculate PCIT implemented in C/C++
refGenes | List of reference genes for 5 different organisms to perform enrichment
RIF | Regulatory Impact Factors (RIF) analysis
RIFPlot | Relationship plots between RIF1, RIF2 and DE genes
RIF_input | Regulatory Impact Factors (RIF) input
runAnalysis | Whole analysis of Regulatory Impact Factors (RIF) and Partial Correlation and Information Theory analysis (PCIT)
simCounts | Simulated counts data
simNorm | Simulated normalized data
SmearPlot | Smear plot for Differentially Expressed genes and TFs
TFs | Transcripition Factors data
tolerance | Tolerance level between 3 pairwise correlations implemented in C/C++