Man pages for kmezhoud/canceR
A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC.

aboutabout canceR
canceRmain function
canceRHelpcanceR Help
canceR_Vignetteopen pdf vignette
cbind.nabind non equal colunm
ClinicalDataClinicalData
dialogGeneClassifierDialogue Box for gene classifier setting: sample size and...
dialoggetGeneListMSigDBMulti-select choice of gene sets from loaded MSigDB
dialogMetOptionDialog Box to set methylation options
dialogMutDialog bos to set returned Mutation information
dialogOptionCircosCheckbox to select dimensions
dialogOptionGSEAlmDialogbox to select variables from Clinical data
dialogOptionPhenoTestCheckbox to select variables from clinical data
dialogPlotOption_SkinCorCheckbox to select variables for plotting
dialogSamplingGSEADialog Box for Sampling patients from expression profile data...
dialogSelectFiles_GSEADialog Box to Select GCT, CLS, GMT and output Files for...
dialogSpecificMutdialog box to Specify Mutation using Regular Expression....
dialogSummary_GSEADialog Box to specify phenotype (variable) used in last...
displayInTableDisplay matrix in tcltk table
GeneExpMatrixGeneExpMatrix
getCasesGet cases for selected Studies. The Cases are the descrption...
getCasesGenProfsget Cases and Genetic Profiles of selected Studies.
getCircosget Circos Layout for selected studies and selected...
getClinicalDataMatrixget matrix with clinical from file
getClinicData_MultipleCasesget Clinical Data for Multiple Cases. User needs to select at...
getCor_ExpCNAMetGet gene correlation for multiple dimensions.
geteSetBuilt Expression Set (eSet) from profile data.
getGCTCLSExampleget GCT and CLS example files.
getGCT_CLSfilesget Profile (GCT file) and Phenotype (CLS file) Data from...
getGeneExpMatrixget matrix with gene expression from file
getGeneListUser needs to specify which gene is interesting to get...
getGeneListExampleget Gene List from examples. User can select one from...
getGeneListFromMSigDBget gene list from MSigDB
getGenesClassifierget Genes Classifier
getGenesTree_MultipleCasesGet successively trees of genes list for multiple cases
getGenesTree_SingleCaseclassify genes in tree for two phenotypes in the same...
getGenProfsGet Genetic Profile from selected Studies
getGSEAlm_Diseasesget GSEA linear modeling by studies (diseases)
getGSEAlm_Variablesget GSEA linear modeling by variables (phenotype)
getInTableget dataframe in TK/TCL table
getListProfDataget a list of Profile Data of every available dimensions....
getMegaProfDataGet profile data for more than 500 genes list.
getMetDataMultipleGenesget Methylation data for multiple genes
getMSigDBReduce MSigDB size for only gene list
getMSigDBExampleget example of .gmt file from MSigDB (Broad Institute)
getMSigDBfileDialog Box to Select MSigDB Files from drive
getMutDataget Mutation data for multiple genes
getPhenoTestAssociate phenotype to Studies (cancers)
getProfilesDataMultipleGenesget Profles Data of multiple genes
getProfilesDataSingleGeneget Profiles Data for a Single Gene.
getSpecificMutget specific Mutation data for multiple genes
getSummaryGSEAget Summary results from GSEA-R (Broad Institute)
getSurvivalSurvival plot
getTextWinget text in tcltk windows
GSEAGSEA-R (Broad Institute)
GSEA.Analyze.SetsGSEA.Analyze.Sets
GSEA.ConsPlotGSEA.ConsPlot
GSEA.EnrichmentScoreGSEA.EnrichmentScore
GSEA.EnrichmentScore2GSEA.EnrichmentScore2
GSEA.Gct2FrameGSEA.Gct2Frame
GSEA.Gct2Frame2GSEA.Gct2Frame2
GSEA.GeneRankingGSEA.GeneRanking
GSEA.HeatMapPlotGSEA.HeatMapPlot
GSEA.HeatMapPlot2GSEA.HeatMapPlot2
GSEA.NormalizeColsGSEA.NormalizeCols
GSEA.NormalizeRowsGSEA.NormalizeRows
GSEA.ReadClsFileGSEA.ReadClsFile
GSEA.Res2FrameGSEA.Res2Frame
GSEA.ThresholdGSEA.Threshold
GSEA.VarFilterGSEA.VarFilter
GSEA.write.gctGSEA.write.gct
Match_GeneList_MSigDBSearch MSigDb that overlap gene list
modalDialogDialog box to specify Gene Symbol.
myGlobalEnvmyGlobalEnv
OLD.GSEA.EnrichmentScoreOLD.GSEA.EnrichmentScore
plot_1Gene_2GenProfsPlotting two genetic profiles for one Gene
plot_2Genes_1GenProfplot correlation of two genes expressions.
plotModelmodel plotting with tcltk
rbind.nabind non equal row
Run.GSEAThe main function to run GSEA-R from Broad Institute
setWorkspaceSetting work Directory and output folders.At starting window,...
testCheckedCaseGenProfTesting checked appropriate Cases for appropriate Genetic...
kmezhoud/canceR documentation built on April 16, 2018, 5:29 p.m.