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


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Documentation for package ‘CeTF’ version 1.19.0

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++