# A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC.

## Documentation for package ‘canceR’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

| 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
dialoggetGeneListMSigDB | Multi-select choice of gene sets from loaded MSigDB
dialogMetOption | dialog box to specify Methylation rate threshold of silencing genes.
dialogMut | dialog box to specify Animo Acid changes using regular expression
dialogOptionCircos | Select with dimensions to plot
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.
getCircos | Get Circos plot of multiple dimensions.
getClinicalDataMatrix | getClinicalDataMatrix
getClinicData_MultipleCases | get Clinical Data for Multiple Cases
getCor_ExpCNAMet | Get gene correlation for multiple dimensions.
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
getGeneListFromMSigDB | Get Gene List from MSigDB.gmt file.
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
getListProfData | get a list of Profile Data of every available dimensions;
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)
getSurvival | Survival plot
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.