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

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Documentation for package ‘CeTF’ version 1.6.0

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

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
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++