Man pages for bitona/MineICA
Analysis of an ICA decomposition obtained on genomics data
| A | Retrieve and set Source S and Mixing matrix A from IcaSet |
| addGenesToGoReport | Add Symbol IDs to hyperGTest results |
| Alist | Retrieve sample contributions stored in an 'IcaSet' object as... |
| annot2Color | Association of a colour with each annotation level |
| annotCarbayo | Carbayo annotation data |
| annotFeatures | Annotation of features using an annotation package |
| annotFeaturesComp | Features annotation |
| annotFeaturesWithBiomaRt | Annotation of features using 'biomaRt' |
| annotInGene | Features annotation of an object of class IcaSet. |
| annotReciprocal | annotReciprocal |
| buildIcaSet | This function builds an object of class 'IcaSet'. |
| buildMineICAParams | Creates an object of class MineICAParams |
| build_sortHeatmap | Build the heatmap matrices |
| class-IcaSet | Class to Contain and Describe an ICA decomposition of... |
| class-MineICAParams | Class to contain parameters for the analysis of an ICA... |
| clusterFastICARuns | Run of fastICA and JADE algorithms |
| clusterSamplesByComp | Cluster samples from an IcaSet |
| clusterSamplesByComp_multiple | Cluster samples from an IcaSet |
| clusVarAnalysis | Tests association between clusters of samples and variables |
| compareAn | Comparison of IcaSet objects using correlation |
| compareAn2graphfile | compareAn2graphfile |
| compareGenes | Union and intersection of contributing genes |
| cor2An | Correlation between two matrices |
| correl2Comp | correl2Comp |
| dat | Retrieve and set data from IcaSet |
| dataCarbayo | Carbayo expression data |
| doEnrichment | Runs enrichment analysis of contributing genes |
| getComp | Retrieve feature and sample values on a component stored in... |
| getProj | Extract projection values |
| getSdExpr | getSdExpr |
| hgOver | Output of 'hyperGtest' |
| hypergeoAn | Runs an enrichment analysis per component using package... |
| icaSetCarbayo | IcaSet-object containing a FastICA decomposition of gene... |
| icaSetKim | IcaSet-object containing a FastICA decomposition of gene... |
| icaSetRiester | IcaSet-object containing a FastICA decomposition of gene... |
| icaSetStransky | IcaSet-object containing a FastICA decomposition of gene... |
| indComp | Retrieve and set component labels, indices, and witness genes... |
| mergeGostatsResults | Merge enrichment results obtained for different databases... |
| nbOccByGeneInComp | nbOccByGeneInComp |
| nbOccInComp | Select components the features contribute to |
| nbOccInComp_simple | nbOccInComp_simple |
| nodeAttrs | Generate node attributes |
| plotAllMix | Plots the Gaussian fitted by 'Mclust' on several numeric... |
| plotCorGraph | Plots graph using |
| plotDens2classInComp_plotOnly | Plots the densities or boxplots of the component... |
| plotDensAllAnnotInAllComp | Tests if groups of samples are differently distributed on the... |
| plotDensOneAnnotInAllComp | Tests if groups of samples are differently distributed on the... |
| plot_heatmapsOnSel | Plot heatmap associated with each component |
| plotMclust | Plots the Gaussian fitted by 'Mclust' |
| plotMix | Plots an histogram and Gaussian fitted by 'Mclust' |
| plotPosAnnotInComp | Histograms of sample contributions for each annotation level |
| plotPosOneAnnotInComp_ggplot | Tests if groups of samples are differently distributed on the... |
| plotPosOneAnnotLevInComp_ggplot | Plots the position of a subset of samples in the histogram of... |
| plotPosSamplesInComp | Histograms of sample subsets |
| qualVarAnalysis | Tests association between qualitative variables and... |
| quantVarAnalysis | Correlation between variables and components. |
| readA | read A |
| readS | read S |
| relativePath | Relative path |
| runAn | Run analysis of an IcaSet object |
| runCompareIcaSets | runCompareIcaSets |
| runEnrich | Enrichment analysis through GOstats |
| runICA | Run of fastICA and JADE algorithms |
| selectContrib | Select contributing features/genes |
| selectFeatures_IQR | Selection of features based on their IQR |
| selectWitnessGenes | selectWitnessGenes |
| Slist | Retrieve feature/gene projections stored in an 'IcaSet'... |
| wilcoxOrKruskalOnA | Comparison of distributions of sample groups |
| writeGenes | Description of features using package 'biomaRt'. |
| writeGostatsHtmltable | Writes enrichment results in a HTML file |
| writeHtmlResTestsByAnnot | Tests if groups of samples are differently distributed on the... |
| writeProjByComp | writeProjByComp |
| writeRnkFiles | Write rnk files containing gene projections |
