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. |