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.
Decifer a 'model parameter' and run appropriate 'glm_...' function.
combiner combines the miRNA and mRNA files
corMirnaRna correlation for miRNA and mRNA
corMirnaRnaMiranda correlation for miRNA and mRNA
This is data is the mRNA FC and miRNA FC correlation data. This data set is used in documentation examples.
downloadMirandaFile Read internal Miranda file
drawCorPlot correlation plots for mRNA and miRNA regression results
drawInterPlots for finInterResult miRNA and mRNA Interrelation real data
fdrSig Ruturns FDR significant miRNA/mRNA predictions
finInterResult miRNA and mRNA interrelation in two-time points results in a dataframe.
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 Makes a list of gene names to be used in the runModels function
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.
Return Miranda data for a given species.
Model functions for GLM with Gaussian model.
Model functions for GLM with negative binomial family.
Model functions for GLM with negative binomial family.
Model functions for GLM with Poisson model.
Model functions for zero inflated model using either Poisson or Negative Binomial distributions.
alias for glm_zeroinfl("negbin")
alias for glm_zeroinfl("poisson")
importMirandaFile Read internal Miranda file
This is data is the mRNA FC and miRNA FC correlation/interaction original data. This data set is used in documentation examples.
This is data is the mRNA expression file. This data set is used in documentation examples.
This is data is the mRNA0_2 FC for 0-2 time point. This data set is used in documentation examples.
This is data is the mRNA0_5 FC for 0-5 time point. This data set is used in documentation examples.
This is data is the mRNA2_5 FC for 2-5 time point. This data set is used in documentation examples.
This is data is the combined mRNA FC for all time points. This data set is used in documentation examples.
This data is the mRNA fold change data set for difference or interrelation section. This data set is used in documentation examples.
makeFormulaRightSide makes right hand side of formula for model variables: vector of indep. variables
This is data is the miRNA expression file. This data set is used in documentation examples.
This is data is the miRNA0_2 FC for 0-2 time point. This data set is used in documentation examples.
This is data is the miRNA0_5 FC for 0-5 time point. This data set is used in documentation examples.
This is data is the miRNA2_5 FC for 2-5 time point. This data set is used in documentation examples.
This is data is the combined miRNA FC for all time points. This data set is used in documentation examples.
This data is the miRNA fold change data set for difference or interrelation section. This data set is used in documentation examples.
miRanComp comparison of mRNAs present with miRanda file targets
This is data is the results file from EBV miRanda getInputSpecies function. This data set is used in documentation examples.
miRandaIntersect Looks for Intersection of Significant output results with miRanda Results from getInputSpeciesDF function
This is data is the results file from mouse miRanda getInputSpecies function. This data set is used in documentation examples.
mirRnaDensityCor for miRTarRNASeq miRNA and mRNA correlation real data versus sampled data
mirRnaDensityInter for mirTarRnaSeq miRNA and mRNA Interrelation real data versus sampled data
mirRnaHeatmap pheatmap for miRTarRNASeq miRNA and mRNA correlation
mirRnaHeatmapDiff heatmap for miRTarRNASeq miRNA and mRNA correlation
mirandaIntersectInter Looks for Intersection of Significant output results with miRanda Results from getInputSpeciesDF function
Transform miRanda data for relevant mRNA and miRNA to matrix form compatible with sponge
Obtain model AIC
Obtain coefficients
Obtain model input data
Obtain model name
Obtain model p-value
Obtain p-values for terms in model formula
modelsFilter Filter a list of models based on logical expression
one2OneRnaMiRNA correlation for miRNA and mRNA using differntial expression fold change and if/when available p-value
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.
This is data is the output file resulted from time point/conditions background correlation model. This data set is used in documentation examples.
This is data is the output file resulted from time point/conditions background difference/interelation model. This data set is used in documentation examples.
Plot model
Plot residuals
plotTerms
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 runModel for all miRNAs
Run a model of a specific kind
runModels runs miRNA mrna model model for various miRNA-mRNA data distributions
sampCorRnaMirna sampling for correlation for miRNA and mRNA
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.
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.
This is data is the results file from regression analysis and its estimates. This data set is used in documentation examples.
threshSig Using shuffling threshold finds appropriate significant miRNA-mRNA correlation
threshSigInter Using shuffling threshold finds appropriate significant miRNA-mRNA correlation
twoTimePoint miRNA and mRNA interrelation in two timepoints
twoTimePointSamp miRNA and mRNA interrelation in two timepoints sampling
tzTransTranspose and z-score transformation