Man pages for kmezhoud/canceR
A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC
| about | about canceR |
| canceR | main function |
| canceR_Issue | canceR Report Issue |
| canceR_Vignette | open pdf vignette |
| cbind.na | bind non equal colunm |
| CGDS | CGDS connect object to cBioPortal |
| dialogGeneClassifier | Dialogue Box for gene classifier setting: sample size and... |
| dialoggetGeneListMSigDB | Multi-select choice of gene sets from loaded MSigDB |
| dialogMetOption | Dialog Box to set methylation options |
| dialogMut | Dialog bos to set returned Mutation information |
| dialogOptionCircos | Checkbox to select dimensions |
| dialogOptionGSEAlm | Dialogbox to select variables from Clinical data |
| dialogOptionPhenoTest | Checkbox to select variables from clinical data |
| dialogPlotOption_SkinCor | Checkbox to select variables for plotting |
| dialogSamplingGSEA | Dialog Box for Sampling patients from expression profile data... |
| dialogSelectFiles_GSEA | Dialog Box to Select GCT, CLS, GMT and output Files for... |
| dialogSpecificMut | dialog box to Specify Mutation using Regular Expression.... |
| dialogSummary_GSEA | Dialog Box to specify phenotype (variable) used in last... |
| displayInTable | Display matrix in tcltk table |
| getCases | Get cases for selected Studies. The Cases are the descrption... |
| getCasesGenProfs | get Cases and Genetic Profiles of selected Studies. |
| getCircos | get Circos Layout for selected studies and selected... |
| getClinicalDataMatrix | get matrix with clinical from file |
| getClinicData_MultipleCases | get Clinical Data for Multiple Cases. User needs to select at... |
| getCor_ExpCNAMet | Get gene correlation for multiple dimensions. |
| geteSet | Built Expression Set (eSet) from profile data. |
| getFreqMutData | get mutation frequency |
| getGCTCLSExample | get GCT and CLS example files. |
| getGCT_CLSfiles | get Profile (GCT file) and Phenotype (CLS file) Data from... |
| getGeneExpMatrix | get matrix with gene expression from file |
| getGeneList | User needs to specify which gene is interesting to get... |
| getGeneListExample | get Gene List from examples. User can select one from... |
| getGeneListFromMSigDB | get gene list from MSigDB |
| getGenesClassifier | get Genes Classifier |
| getGenesTree_MultipleCases | Get successively trees of genes list for multiple cases |
| getGenesTree_SingleCase | classify genes in tree for two phenotypes in the same... |
| getGenProfs | Get Genetic Profile from selected Studies |
| getGSEAlm_Diseases | get GSEA linear modeling by studies (diseases) |
| getGSEAlm_Variables | get GSEA linear modeling by variables (phenotype) |
| getInTable | get dataframe in TK/TCL table |
| getListProfData | Get list of data frame with profiles data (CNA,mRNA,... |
| getMegaProfData | Get profile data for more than 500 genes list. |
| getMetDataMultipleGenes | get Methylation data for multiple genes |
| getMSigDB | Reduce MSigDB size for only gene list |
| getMSigDBExample | get example of .gmt file from MSigDB (Broad Institute) |
| getMSigDBfile | Dialog Box to Select MSigDB Files from drive |
| getMutData | get Mutation data for multiple genes |
| getPhenoTest | Associate phenotype to Studies (cancers) |
| getProfData | Search and get genetic profiles (CNA,mRNA, Methylation,... |
| getProfilesDataMultipleGenes | get Profles Data of multiple genes |
| getProfilesDataSingleGene | get Profiles Data for a Single Gene. |
| getSpecificMut | get specific Mutation data for multiple genes |
| getSummaryGSEA | get Summary results from GSEA-R (Broad Institute) |
| getSurvival | Survival plot |
| getTextWin | get text in tcltk windows |
| 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 | Search MSigDb that overlap gene list |
| modalDialog | Dialog box to specify Gene Symbol. |
| myGlobalEnv | myGlobalEnv |
| OLD.GSEA.EnrichmentScore | OLD.GSEA.EnrichmentScore |
| plot_1Gene_2GenProfs | Plotting two genetic profiles for one Gene |
| plot_2Genes_1GenProf | plot correlation of two genes expressions. |
| plotModel | model plotting with tcltk |
| rbind.na | bind non equal row |
| Run.GSEA | The main function to run GSEA-R from Broad Institute |
| setWorkspace | Setting work Directory and output folders.At starting window,... |
| test.CGDS | S3 method to test cBioPortal connection |
| testCheckedCaseGenProf | Testing checked appropriate Cases for appropriate Genetic... |
| UnifyRowNames | Unify row names in data frame with the same order of gene... |
