# mirTarRnaSeq

## Documentation for package ‘mirTarRnaSeq’ version 1.14.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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