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


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Documentation for package ‘canceR’ version 1.0.0

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
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.