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