Skip to main content

Table 1 Functions available in CeTF

From: CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis

Function Description
bivar.awk Summary statistics from two variables
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
getDE 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
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
normExp Normalized expression transformation
OutputData 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_input Regulatory Impact Factors (RIF) input
RIF Regulatory Impact Factors (RIF) analysis
RIFPlot Relationship plots between RIF1, RIF2 and DE genes
runAnalysis Whole analysis of RIF and 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++