| canonicalModel_ |
Decifer a 'model parameter' and run appropriate 'glm_...' function. |
| 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. |
| 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 |
| 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. |
| finInterResult |
finInterResult miRNA and mRNA interrelation in two-time points results in a dataframe. |
| 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. |
| makeFormulaRightSide |
makeFormulaRightSide makes right hand side of formula for model variables: vector of indep. variables |
| 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 |
| mirandaIntersectInter |
mirandaIntersectInter 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. |
| miranda_sponge_predict |
Transform miRanda data for relevant mRNA and miRNA to matrix form compatible with sponge |
| 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. |
| 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 |
| modelAIC |
Obtain model AIC |
| modelCoefficients |
Obtain coefficients |
| modelData |
Obtain model input data |
| modelModelName |
Obtain model name |
| modelModelPvalue |
Obtain model p-value |
| modelsFilter |
modelsFilter Filter a list of models based on logical expression |
| modelTermPvalues |
Obtain p-values for terms in model formula |
| 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. |
| 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. |
| one2OneRnaMiRNA |
one2OneRnaMiRNA correlation for miRNA and mRNA using differntial expression fold change and if/when available p-value |
| 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_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. |
| 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. |
| 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 |
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