Man pages for mariavica/mircomb
An R package for analyzing miRNA-mRNA interactions
| addCorrelation | Correlate miRNA and mRNA expression |
| addCorrelation.R | Correlation, old version |
| addDatabase | Intersect correlations with an external database. |
| addDiffexp | Calculate differential expression |
| addFoldchanges | Add foldchanges to the 'net' slot |
| addGlmnet | Add elastic net estimates |
| addLong | Time analysis |
| addNet | Create a net slot |
| addScore | Create a score |
| addSig | Select significant miRNAs or mRNAs |
| addSurv | Calculate hazard ratio |
| boxplotCorrelation | Plot boxplot and correlation of a miRNA-mRNA pair |
| boxplotSamples | Boxplots of samples expression |
| checkmiRNAs | Compare a list of miRNAs with different miRBase versions |
| combinePval | Combine _p_ values |
| corObject-class | Class '"corObject"' |
| correctPval | Correct _p_ values |
| data.obj | Example of a 'corObject' |
| evaluate | Evaluate function |
| GOanalysis | GO and KEGG enrichment analysis |
| information-package | Find miRNA targets combining both biological and theoretical... |
| miRNA | miRNA data expression |
| mkReport | Creates a pdf report |
| mRNA | mRNA data expression |
| openCytoscape | Open cytoscape session with the network of miRNA-mRNA... |
| pearson | Pearson correlation with C++ code |
| pheno.miRNA | Phenotypical miRNA information |
| pheno.mRNA | Phenotypical mRNA information |
| plot3d | PCA plot in 3D |
| plotCircos | Circos plot |
| plotCordist | Plot distances/correlation between miRNA or mRNA samples |
| plotCorrelation | Plot correlations |
| plotDensity | Plot miRNA or mRNA density |
| plotHclust | Plot hierarchical clustering of miRNA or mRNA samples |
| plotHeatmap | Plot heatmaps |
| plotMA | MA plot |
| plotNetwork | Plot a network |
| plotPca | PCA with miRNA or mRNA data |
| plotSurv | Plot Kaplan-Meier curve |
| plotVolcano | Volcano plot |
| removeSamp | Remove samples or miRNA/mRNA |
| selOutliers | select outliers based on PCA analysis |
| selSubsetCor | Select relevant miRNA-mRNA interactions |
| selSubsetExprs | Select differentially expressed miRNAs or mRNAs |
| summary.corObject | Brief report of a 'corObject' |
| topTable | Print or plot the top connected miRNA/mRNA |
| translatemiRNAs | Convert miRNA names between versions |
| writeCsv | Write a csv file |
| writeExcel | Write an Excel file |
| writeSif | Write a SIF file |
