MD-Anderson-Bioinformatics/GeneSurvey
MD Anderson Gene Survey

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Search the MD-Anderson-Bioinformatics/GeneSurvey package
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Functions
319
Source code
118
Man pages
113
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MD-Anderson-Bioinformatics/GeneSurvey: MD Anderson Gene Survey
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API

API for MD-Anderson-Bioinformatics/GeneSurvey
MD Anderson Gene Survey

Global functions
.onAttach Source code
averageWithin Source code
buildGeneReportDataObject_internal Source code
colorDistEval Source code
colorDistance Source code
combineWithin Source code
compressIntoFilename Source code
computeDelta_internal Source code
convertFileToList Source code
dividerRowLabels Source code
filterForCommonSamples Man page Source code
geneReportVersion Source code
geneSymbolsForDataset Man page Source code
geneSymbolsMatchDataset Man page Source code
get.Chromosome Man page
get.Chromosome,ANY-method Man page
get.Chromosome-method Man page
get.Data Man page
get.Data,ANY-method Man page
get.Data-method Man page
get.DerivedFrom Man page
get.DerivedFrom,ANY-method Man page
get.DerivedFrom-method Man page
get.GeneId Man page
get.GeneId,ANY-method Man page
get.GeneId-method Man page
get.GeneStructure Man page
get.GeneStructure,ANY-method Man page
get.GeneStructure-method Man page
get.GeneSymbol Man page
get.GeneSymbol,ANY-method Man page
get.GeneSymbol-method Man page
get.GenomeAnnotations Man page
get.GenomeAnnotations,ANY-method Man page
get.GenomeAnnotations-method Man page
get.LocationEnd Man page
get.LocationEnd,ANY-method Man page
get.LocationEnd-method Man page
get.LocationStart Man page
get.LocationStart,ANY-method Man page
get.LocationStart-method Man page
get.MimatId Man page
get.MimatId,ANY-method Man page
get.MimatId-method Man page
get.MirId Man page
get.MirId,ANY-method Man page
get.MirId-method Man page
get.MirType Man page
get.MirType,ANY-method Man page
get.MirType-method Man page
get.Name Man page
get.Name,ANY-method Man page
get.Name-method Man page
get.ProbeLocation Man page
get.ProbeLocation,ANY-method Man page
get.ProbeLocation-method Man page
get.SampleAnnotations Man page
get.SampleAnnotations,ANY-method Man page
get.SampleAnnotations-method Man page
get.Strand Man page
get.Strand,ANY-method Man page
get.Strand-method Man page
get.TissueAnnotations Man page
get.TissueAnnotations,ANY-method Man page
get.TissueAnnotations-method Man page
get.VersionIndex Man page
get.VersionIndex,ANY-method Man page
get.VersionIndex-method Man page
getBaseDir Man page Source code
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_MutationDetails Man page 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
getExons_GeneEq_internal Source code
getExons_GeneSymbol_HG19 Man page Source code
getImputedNAs_CombinedHsaMimat_miRNASeq Man page
getImputedNAs_GeneSymbol_RnaSeq Man page
getImputedNAs_GeneSymbol_RnaSeq2 Man page
getImputedNAs_GeneSymbol_SNP6 Man page
getImputedNAs_Probe_Meth27 Man page
getImputedNAs_Probe_Meth450 Man page
getMaxEnd 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
getMinStart 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
getMutationDetails_Dataframe Man page 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_Mutation_Details 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
getPlotSymbol Source code
getSynonyms Man page Source code
getTranscriptEnd Source code
getTranscriptStart Source code
getTranscriptSymbols Source code
getTranscripts_GeneEq_internal Source code
getTranscripts_GeneSymbol_HG19 Man page Source code
getZipDir Man page Source code
initGeneReport Man page Source code
isValidDirectoryPath Source code
loadDataObject Man page Source code
loadGeneMutationDetails Source code
makeSilentNonsilent 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
plotGeneArchitecture Source code
plotGenericOutput Man page Source code
plotHeatmapOutput Man page Source code
plotMutations_aminoacid Source code
plotMutations_dna 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
readAsGenericDataframe_internal Source code
readMatrix_internal Source code
readTissueAnnotations_internal Source code
replicateValues Source code
rowLabelNumbersFromLabels Source code
setJavaVerboseFlag Source code
simplifyRowLabels Source code
stripchartAcrossDiseases Source code
testColors Source code
verboseMessage Source code
MD-Anderson-Bioinformatics/GeneSurvey documentation built on May 7, 2019, 2:04 p.m.

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