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

## Documentation for package ‘canceR’ version 1.45.0

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

## Help Pages

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 postprob threshold
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 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 to Specify Mutation using Regular Expression. Search specific mutation using regular expression.
dialogSummary_GSEA | Dialog Box to specify phenotype (variable) used in last GSEA-R to get Summary Results. This function ask the user to specify the phenotype (variable).
displayInTable | Display matrix in tcltk table
getCases | Get cases for selected Studies. The Cases are the descrption of the samples from patients. The samples can be subdivided by the type of assays as, sequencing, CNA, Mutation, Methylation.
getCasesGenProfs | get Cases and Genetic Profiles of selected Studies.
getCircos | get Circos Layout for selected studies and selected dimensions
getClinicalDataMatrix | get matrix with clinical from file
getClinicData_MultipleCases | get Clinical Data for Multiple Cases. User needs to select at least one case to run this function. Get clinical data for more one or multiple cases.
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 Disease.
getGeneExpMatrix | get matrix with gene expression from file
getGeneList | User needs to specify which gene is interesting to get genomic cancer data. The gene must be with Symbol and one gene by line.
getGeneListExample | get Gene List from examples. User can select one from available gene list
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 case(disease).
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, Methylation, Mutation...)
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, Mutation...)
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
plotModel | model plotting with tcltk
plot_1Gene_2GenProfs | Plotting two genetic profiles for one Gene
plot_2Genes_1GenProf | plot correlation of two genes expressions.
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, user needs to set work directory for output data. The function is foud in File menu.
test.CGDS | S3 method to test cBioPortal connection
testCheckedCaseGenProf | Testing checked appropriate Cases for appropriate Genetic profiles.
UnifyRowNames | Unify row names in data frame with the same order of gene list.