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


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Documentation for package ‘canceR’ version 1.21.0

Help Pages

about about canceR
canceR main function
canceRHelp canceR Help
canceR_Vignette open pdf vignette
cbind.na bind non equal colunm
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.
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 a list of Profile Data of every available dimensions. This function load matrices of every dimension (Exp, CNA, Met, RPPA,miRNA,Mut) and save them in a list for every disease.
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)
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.
testCheckedCaseGenProf Testing checked appropriate Cases for appropriate Genetic profiles.