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| Main function of canceR package. | |
| about | get brief information and help. |
| canceR | Main function of canceR package. |
| canceRHelp | canceRHelp |
| canceR_Vignette | Get Vignette |
| cbind.na | cbind.na |
| ClinicalData | ClinicalData |
| dialogGeneClassifier | dialogGeneClassifier |
| dialogMetOption | dialog box to specify Methylation rate threshold of silencing genes. |
| dialogMut | dialog box to specify Animo Acid changes using regular expression |
| dialogOptionGSEAlm | Dialog Box Option for GSEAlm |
| dialogOptionPhenoTest | Dialog Box to specify Variables for PhenoTest function. |
| dialogPlotOption_SkinCor | dialogPlotOption_SkinCor |
| dialogSamplingGSEA | Dialog Box for Sampling patients from expression profile data used for GSEA-R (Broad Institute) |
| dialogSelectFiles_GSEA | Dialog Box to Select GCT, CLS, GMT and output Files for GSEA-R (Broad Institute) |
| dialogSpecificMut | dialog box tp Specify Mutation using Regular Expression. |
| dialogSummary_GSEA | Dialog Box to specify phenotype (variable) used in last GSEA-R to get Summary Results. |
| displayInTable | Display In Table |
| GeneExpMatrix | Profile data |
| getCases | Get cases for selected Studies |
| getCasesGenProfs | get Cases and Genetic Profiles of selected Studies. |
| getClinicalDataMatrix | getClinicalDataMatrix |
| getClinicData_MultipleCases | get Clinical Data for Multiple Cases |
| geteSet | Build expression Set (Biobase) |
| getGCTCLSExample | getGCTCLSExample |
| getGCT_CLSfiles | get Profile (GCT file) and Phenotype (CLS file) Data from Disease. |
| getGeneExpMatrix | load matrix from file |
| getGeneList | get Gene List from file. |
| getGeneListExample | get Gene List from examples |
| getGenesClassifier | Ranking Genes by Diseases. |
| getGenesTree_MultipleCases | getGenesTree_MultipleCases |
| getGenesTree_SingleCase | getGenesTree_SingleCase |
| getGenProfs | Get Genetic Profile from selected Studies |
| getGSEAlm_Diseases | Get Gene Set Enrichment Analysis linear modeling for two Diseases. |
| getGSEAlm_Variables | Get Gene Set Enrichment Analysis linear modeling for two phenotypes (variables) in the same disease. |
| getInTable | getInTable |
| getMegaProfData | getMegaProfData |
| getMetDataMultipleGenes | get Methylation Data for Multiple Genes. |
| getMSigDB | getMSigDB |
| getMSigDBExample | getMSigDBExample |
| getMSigDBfile | getMSigDBfile |
| getMutData | get Mutation Data for gene list. |
| getPhenoTest | Associate Phenotypes (variables) from Clinical data to gene expression profile. |
| getProfilesDataMultipleGenes | get Profiles Data of Multiple Genes. |
| getProfilesDataSingleGene | get Profiles Data for a Single Gene. |
| getSpecificMut | get Specific Mutation using Amino Acid changes. |
| getSummaryGSEA | get Summary results from GSEA-R (Broad Institute) |
| getTextWin | getTextWin |
| GSEA | GSEA-R (Broad Institute) |
| GSEA.Analyze.Sets | GSEA.Analyze.Sets |
| GSEA.ConsPlot | GSEA.ConsPlot |
| GSEA.EnrichmentScore | GSEA.EnrichmentScore |
| GSEA.EnrichmentScore2 | GSEA.EnrichmentScore2 |
| GSEA.Gct2Frame | GSEA.Gct2Frame |
| GSEA.Gct2Frame2 | GSEA.Gct2Frame2 |
| GSEA.GeneRanking | GSEA.GeneRanking |
| GSEA.HeatMapPlot | GSEA.HeatMapPlot |
| GSEA.HeatMapPlot2 | GSEA.HeatMapPlot2 |
| GSEA.NormalizeCols | GSEA.NormalizeCols |
| GSEA.NormalizeRows | GSEA.NormalizeRows |
| GSEA.ReadClsFile | GSEA.ReadClsFile |
| GSEA.Res2Frame | GSEA.Res2Frame |
| GSEA.Threshold | GSEA.Threshold |
| GSEA.VarFilter | GSEA.VarFilter |
| GSEA.write.gct | GSEA.write.gct |
| Match_GeneList_MSigDB | Match_GeneList_MSigDB |
| modalDialog | Dialog box to specify Gene Symbol. |
| myGlobalEnv | myGlobalEnv |
| OLD.GSEA.EnrichmentScore | OLD.GSEA.EnrichmentScore |
| plotModel | plot Model |
| plot_1Gene_2GenProfs | Plotting two genetic profiles for one Gene |
| plot_2Genes_1GenProf | plot correlation of two genes expressions. |
| rbind.na | rbind.na |
| Run.GSEA | The main function to run GSEA-R from Broad Institute |
| setWorkspace | Setting work Directory and output folders. |
| testCheckedCaseGenProf | Testing checked appropriate Cases for appropriate Genetic profiles. |