Combine                 This is data is the mRNA expression across
                        samples and miRNA expression data which is to
                        be investigated in one file. This data set is
                        used in documentation examples.
canonicalModel_         Decifer a 'model parameter' and run appropriate
                        'glm_...' function.
combiner                combiner combines the miRNA and mRNA files
corMirnaRna             corMirnaRna correlation for miRNA and mRNA
corMirnaRnaMiranda      corMirnaRnaMiranda correlation for miRNA and
                        mRNA
corr_0                  This is data is the mRNA FC and miRNA FC
                        correlation data. This data set is used in
                        documentation examples.
downloadMirandaFile     downloadMirandaFile Read internal Miranda file
drawCorPlot             drawCorPlot correlation plots for mRNA and
                        miRNA regression results
drawInterPlots          drawInterPlots for finInterResult miRNA and
                        mRNA Interrelation real data
fdrSig                  fdrSig Ruturns FDR significant miRNA/mRNA
                        predictions
finInterResult          finInterResult miRNA and mRNA interrelation in
                        two-time points results in a dataframe.
final_results           This is data is the mRNA FC and miRNA FC
                        correlation/interaction data results after
                        filteration. This data set is used in
                        documentation examples.
geneVari                geneVari Makes a list of gene names to be used
                        in the runModels function
geneVariant             This is data is the mRNA expression across
                        samples and miRNA expression data which is to
                        be investigated giving directions on which data
                        is miRNA and which is mRNA. This data set is
                        used in documentation examples.
getInputSpecies         Return Miranda data for a given species.
glm_gaussian            Model functions for GLM with Gaussian model.
glm_multi               Model functions for GLM with negative binomial
                        family.
glm_nb                  Model functions for GLM with negative binomial
                        family.
glm_poisson             Model functions for GLM with Poisson model.
glm_zeroinfl            Model functions for zero inflated model using
                        either Poisson or Negative Binomial
                        distributions.
glm_zeroinfl_negbin     alias for glm_zeroinfl("negbin")
glm_zeroinfl_poisson    alias for glm_zeroinfl("poisson")
importMirandaFile       importMirandaFile Read internal Miranda file
inter0                  This is data is the mRNA FC and miRNA FC
                        correlation/interaction original data. This
                        data set is used in documentation examples.
mRNA                    This is data is the mRNA expression file. This
                        data set is used in documentation examples.
mRNA0_2                 This is data is the mRNA0_2 FC for 0-2 time
                        point. This data set is used in documentation
                        examples.
mRNA0_5                 This is data is the mRNA0_5 FC for 0-5 time
                        point. This data set is used in documentation
                        examples.
mRNA2_5                 This is data is the mRNA2_5 FC for 2-5 time
                        point. This data set is used in documentation
                        examples.
mRNA_fc                 This is data is the combined mRNA FC for all
                        time points. This data set is used in
                        documentation examples.
mRNA_fc2                This data is the mRNA fold change data set for
                        difference or interrelation section. This data
                        set is used in documentation examples.
makeFormulaRightSide    makeFormulaRightSide makes right hand side of
                        formula for model variables: vector of indep.
                        variables
miRNA                   This is data is the miRNA expression file. This
                        data set is used in documentation examples.
miRNA0_2                This is data is the miRNA0_2 FC for 0-2 time
                        point. This data set is used in documentation
                        examples.
miRNA0_5                This is data is the miRNA0_5 FC for 0-5 time
                        point. This data set is used in documentation
                        examples.
miRNA2_5                This is data is the miRNA2_5 FC for 2-5 time
                        point. This data set is used in documentation
                        examples.
miRNA_fc                This is data is the combined miRNA FC for all
                        time points. This data set is used in
                        documentation examples.
miRNA_fc2               This data is the miRNA fold change data set for
                        difference or interrelation section. This data
                        set is used in documentation examples.
miRanComp               miRanComp comparison of mRNAs present with
                        miRanda file targets
miRanda                 This is data is the results file from EBV
                        miRanda getInputSpecies function. This data set
                        is used in documentation examples.
miRandaIntersect        miRandaIntersect Looks for Intersection of
                        Significant output results with miRanda Results
                        from getInputSpeciesDF function
miRandaM                This is data is the results file from mouse
                        miRanda getInputSpecies function. This data set
                        is used in documentation examples.
mirRnaDensityCor        mirRnaDensityCor for miRTarRNASeq miRNA and
                        mRNA correlation real data versus sampled data
mirRnaDensityInter      mirRnaDensityInter for mirTarRnaSeq miRNA and
                        mRNA Interrelation real data versus sampled
                        data
mirRnaHeatmap           mirRnaHeatmap pheatmap for miRTarRNASeq miRNA
                        and mRNA correlation
mirRnaHeatmapDiff       mirRnaHeatmapDiff heatmap for miRTarRNASeq
                        miRNA and mRNA correlation
mirandaIntersectInter   mirandaIntersectInter Looks for Intersection of
                        Significant output results with miRanda Results
                        from getInputSpeciesDF function
miranda_sponge_predict
                        Transform miRanda data for relevant mRNA and
                        miRNA to matrix form compatible with sponge
modelAIC                Obtain model AIC
modelCoefficients       Obtain coefficients
modelData               Obtain model input data
modelModelName          Obtain model name
modelModelPvalue        Obtain model p-value
modelTermPvalues        Obtain p-values for terms in model formula
modelsFilter            modelsFilter Filter a list of models based on
                        logical expression
one2OneRnaMiRNA         one2OneRnaMiRNA correlation for miRNA and mRNA
                        using differntial expression fold change and
                        if/when available p-value
one2manySponge          Sparse Partial Correlations On mRNA/miRNA
                        Expression We make mirTarRnaSeq compatible to
                        SPONGE package in order to estimate sparse
                        matrix correlation (using elstic net) for
                        prediction potential miRNA-mRNA interaction.
                        Note this function/method is suggested for
                        miRNA/mRNA interactions in many samples with a
                        notable variance of mRNA/miRNA expression. This
                        model also only reports negative sparse partial
                        correlation predictions.
outs                    This is data is the output file resulted from
                        time point/conditions background correlation
                        model. This data set is used in documentation
                        examples.
outs2                   This is data is the output file resulted from
                        time point/conditions background
                        difference/interelation model. This data set is
                        used in documentation examples.
plotFit                 Plot model
plotResiduals           Plot residuals
plotTerms               plotTerms
results                 This is data is the output file resulted from
                        time point or conditions or correlation or
                        interrelation model. This data set is used in
                        documentation examples.
runAllMirnaModels       runAllMirnaModels runModel for all miRNAs
runModel                Run a model of a specific kind
runModels               runModels runs miRNA mrna model model for
                        various miRNA-mRNA data distributions
sampCorRnaMirna         sampCorRnaMirna sampling for correlation for
                        miRNA and mRNA
sig_InterR              This is data is the output file resulted from
                        time point or conditions experiment for
                        interrelation model after filtering and
                        threshold modification. This data set is used
                        in documentation examples.
sig_corrs               This is data is the output file resulted from
                        time point or conditions experiment for
                        correlation model after filtering and threshold
                        modification. This data set is used in
                        documentation examples.
some_model              This is data is the results file from
                        regression analysis and its estimates. This
                        data set is used in documentation examples.
threshSig               threshSig Using shuffling threshold finds
                        appropriate significant miRNA-mRNA correlation
threshSigInter          threshSigInter Using shuffling threshold finds
                        appropriate significant miRNA-mRNA correlation
twoTimePoint            twoTimePoint miRNA and mRNA interrelation in
                        two timepoints
twoTimePointSamp        twoTimePointSamp miRNA and mRNA interrelation
                        in two timepoints sampling
tzTrans                 tzTransTranspose and z-score transformation
