API for GeneSurvey/TCGAGeneReport
Access to Gene Report Data

Global functions
buildGeneReportDataObject_internal Source code
colorDistEval Source code
colorDistance Source code
compressIntoFilename Source code
computeDelta_internal Source code
convertFileToList Source code
filterForCommonSamples Man page Source code
geneSymbolsForDataset Man page Source code
geneSymbolsMatchDataset Man page Source code
get.Chromosome Man page
get.Data Man page
get.DerivedFrom Man page
get.GeneId Man page
get.GeneStructure Man page
get.GeneSymbol Man page
get.GenomeAnnotations Man page
get.LocationEnd Man page
get.LocationStart Man page
get.MimatId Man page
get.MirId Man page
get.MirType Man page
get.Name Man page
get.ProbeLocation Man page
get.SampleAnnotations Man page
get.Strand Man page
get.TissueAnnotations Man page
get.VersionIndex Man page
getColorList Source code
getColorListAny Source code
getColorsDistance Source code
getColorsForDiseases Man page Source code
getContrast Man page Source code
getContrastData Source code
getCorByDisease Source code
getDataClinical Man page Source code
getDataClinical_internal Source code
getDataDelta_internal Source code
getDataMatrix_GeneSymbol_Meth27 Man page Source code
getDataMatrix_GeneSymbol_Meth450 Man page Source code
getDataObj_internal Source code
getDataObject_CombinedHsaMimat_miRNASeq Man page Source code
getDataObject_GeneSymbol_Meth27 Man page Source code
getDataObject_GeneSymbol_Meth450 Man page Source code
getDataObject_GeneSymbol_Mutations Man page Source code
getDataObject_GeneSymbol_RnaSeq Man page Source code
getDataObject_GeneSymbol_RnaSeq2 Man page Source code
getDataObject_GeneSymbol_SNP6 Man page Source code
getDataObject_Probe_Meth27 Man page Source code
getDataObject_Probe_Meth450 Man page Source code
getDataPlatform_CombinedHsaMimat_miRNASeq Man page Source code
getDataPlatform_GeneSymbol_Mutations Man page Source code
getDataPlatform_GeneSymbol_RnaSeq Man page Source code
getDataPlatform_GeneSymbol_RnaSeq2 Man page Source code
getDataPlatform_GeneSymbol_SNP6 Man page Source code
getDataPlatform_Probe_Meth27 Man page Source code
getDataPlatform_Probe_Meth450 Man page Source code
getDataPlatform_internal Source code
getDataVersion Man page Source code
getData_CombinedHsaMimat_miRNASeq Man page Source code
getData_GeneEq_internal Source code
getData_GeneSymbol_Mutations Man page Source code
getData_GeneSymbol_RnaSeq Man page Source code
getData_GeneSymbol_RnaSeq2 Man page Source code
getData_GeneSymbol_SNP6 Man page Source code
getData_Probe_Meth27 Man page Source code
getData_Probe_Meth450 Man page Source code
getDelta_Meth27 Source code
getDelta_Meth450 Source code
getDelta_Mutations Source code
getDelta_RnaSeq Source code
getDelta_RnaSeq2 Source code
getDelta_SNP6 Source code
getDelta_miRNASeq Source code
getDiseaseData Source code
getImputedNAs_CombinedHsaMimat_miRNASeq Man page Source code
getImputedNAs_GeneEq_internal Source code
getImputedNAs_GeneSymbol_RnaSeq Man page Source code
getImputedNAs_GeneSymbol_RnaSeq2 Man page Source code
getImputedNAs_GeneSymbol_SNP6 Man page Source code
getImputedNAs_Probe_Meth27 Man page Source code
getImputedNAs_Probe_Meth450 Man page Source code
getMetadataPop_BarcodeDisease Man page Source code
getMetadataPop_BarcodeDisease_forList Source code
getMetadataPop_BarcodeSamplecode Man page Source code
getMetadataPop_BarcodeSamplecode_forList Source code
getMetadataPop_PatientDisease Man page Source code
getMetadataPop_PatientDisease_forList Source code
getMetadataPop_internal Source code
getMetadataTcga_Name_Dataset Source code
getMetadataTcga_Name_Disease Source code
getMetadataTcga_Name_SampleType Source code
getMetadataTcga_Name_internal Source code
getMetadata_GeneByNeighbor_HG18 Man page Source code
getMetadata_GeneByNeighbor_HG19 Man page Source code
getMetadata_GeneByNeighbor_RnaSeq Man page Source code
getMetadata_GeneByNeighbor_RnaSeq2 Man page Source code
getMetadata_Gene_HG18 Man page Source code
getMetadata_Gene_HG19 Man page Source code
getMetadata_Gene_JavaToR Source code
getMetadata_Gene_Mutations Man page Source code
getMetadata_Gene_RnaSeq Man page Source code
getMetadata_Gene_RnaSeq2 Man page Source code
getMetadata_Gene_internal Source code
getMetadata_HG_JavaToR Source code
getMetadata_HG_internal Source code
getMetadata_ProbeByNeighbor_Meth27 Man page Source code
getMetadata_ProbeByNeighbor_Meth450 Man page Source code
getMetadata_Probe_JavaToR Source code
getMetadata_Probe_Meth27 Man page Source code
getMetadata_Probe_Meth450 Man page Source code
getMetadata_Probe_internal Source code
getMirs_List_Mimat Man page Source code
getMirs_List_Mir Man page Source code
getMirs_List_internal Source code
getMirs_Metadata_Mimat Man page Source code
getMirs_Metadata_Mir Man page Source code
getMirs_Metadata_internal Source code
getNamesFromMapping_internal Source code
getNames_CombinedHsaMimat_miRNASeq Man page Source code
getNames_GeneSymbol_Meth27 Man page Source code
getNames_GeneSymbol_Meth450 Man page Source code
getNames_GeneSymbol_Mutations Man page Source code
getNames_GeneSymbol_RnaSeq Man page Source code
getNames_GeneSymbol_RnaSeq2 Man page Source code
getNames_GeneSymbol_SNP6 Man page Source code
getNames_ProbeFromGeneSymbol_Meth27 Man page Source code
getNames_ProbeFromGeneSymbol_Meth450 Man page Source code
getNames_ProbeFromGeneSymbol_internal Source code
getNames_Probe_Meth27 Man page Source code
getNames_Probe_Meth450 Man page Source code
getNames_internal Source code
getOneToOne_GeneSymbol_List Man page Source code
getOneToOne_GeneSymbol_UCID Man page Source code
getOneToOne_List_internal Source code
getOneToOne_Name_internal Source code
getOneToOne_UCID_GeneSymbol Man page Source code
getOneToOne_UCSC_List Man page Source code
getSynonyms Man page Source code
initGeneReport Man page Source code
isValidDirectoryPath Source code
loadDataObject Man page Source code
matrixWithIssues Source code
mycolors Source code
padChromosomeName Source code
plotAssayByDisease Source code
plotAssayForDisease Source code
plotAssays Man page Source code
plotCorByDisease Source code
plotGenericOutput Man page Source code
plotHeatmapOutput Man page Source code
plot_CombinedHsaMimat_miRNASeq Man page Source code
plot_GeneSymbol_Meth27 Man page Source code
plot_GeneSymbol_Meth450 Man page Source code
plot_GeneSymbol_Mutations Man page Source code
plot_GeneSymbol_RnaSeq Man page Source code
plot_GeneSymbol_RnaSeq2 Man page Source code
plot_GeneSymbol_SNP6 Man page Source code
plot_Probe_Meth27 Man page Source code
plot_Probe_Meth450 Man page Source code
plot_fromGene_internal Source code
readAsGenericMatrix Source code
readGeneAnnotations_internal Source code
readHsaMimatAnnotations_internal Source code
readMatrix_internal Source code
readProbeAnnotations_internal Source code
readSampleAnnotations_internal Source code
readTissueAnnotations_internal Source code
replicateValues Source code
setJavaVerboseFlag Source code
stripchartAcrossDiseases Source code
testColors Source code
verboseMessage Source code
GeneSurvey/TCGAGeneReport documentation built on May 8, 2017, noon