API for zwdzwd/sesame
SEnsible Step-wise Analysis of DNA MEthylation BeadChips
| Global functions | |
|---|---|
| .backgroundCorrCh1 | Source code |
| .onAttach | Source code |
| .setGroup_betas | Source code |
| .setGroup_channel | Source code |
| .setGroup_detection | Source code |
| .setGroup_dyeBias | Source code |
| .setGroup_intensity | Source code |
| .setGroup_numProbes | Source code |
| BetaValueToMValue | Man page Source code |
| DMGetProbeInfo | Source code |
| DML | Man page Source code |
| DMLpredict | Man page Source code |
| DMR | Man page Source code |
| ELBAR | Man page Source code |
| InfI | Source code |
| InfIG | Source code |
| InfII | Source code |
| InfIR | Source code |
| KYCG_annoProbes | Man page Source code |
| KYCG_buildGeneDBs | Man page Source code |
| KYCG_getDBs | Man page Source code |
| KYCG_listDBGroups | Man page Source code |
| KYCG_loadDBs | Man page Source code |
| KYCG_plotBar | Man page Source code |
| KYCG_plotDot | Man page Source code |
| KYCG_plotEnrichAll | Man page Source code |
| KYCG_plotLollipop | Man page Source code |
| KYCG_plotManhattan | Man page Source code |
| KYCG_plotMeta | Man page Source code |
| KYCG_plotMetaEnrichment | Man page Source code |
| KYCG_plotPointRange | Man page Source code |
| KYCG_plotSetEnrichment | Man page Source code |
| KYCG_plotVolcano | Man page Source code |
| KYCG_plotWaterfall | Man page Source code |
| MValueToBetaValue | Man page Source code |
| SDFcollapseToPfx | Man page Source code |
| SigDF | Man page Source code |
| SigSetToSigDF | Source code |
| addMask | Man page Source code |
| aggregateTestEnrichments | Man page Source code |
| assemble_plots | Man page Source code |
| backgroundCorrectionNoobFit | Source code |
| betaMix2States | Source code |
| betaMix3States | Source code |
| betasCollapseToPfx | Man page Source code |
| binReadNumeric | Source code |
| binSignals | Man page Source code |
| binWriteNumeric | Source code |
| bisConversionControl | Man page Source code |
| calcES_Significance | Source code |
| calcEffectSize | Man page Source code |
| calcMode | Source code |
| checkLevels | Man page Source code |
| chipAddressToSignal | Man page Source code |
| cleanRefSet | Source code |
| clusterWithSampleGrouping | Source code |
| clusterWithSignature | Source code |
| clusterWithinRowGroups | Source code |
| cnSegmentation | Man page Source code |
| cnv_normal_default | Source code |
| cnv_plot_extra | Source code |
| compareDatbaseSetOverlap | Man page Source code |
| compareMouseStrainReference | Man page Source code |
| compareMouseTissueReference | Man page Source code |
| compareReference | Man page Source code |
| controls | Man page Source code |
| convertProbeID | Man page Source code |
| createDBNetwork | Man page Source code |
| createUCSCtrack | Man page Source code |
| create_default_mask | Source code |
| dataFrame2sesameQC | Man page Source code |
| databases_getMeta | Source code |
| dbStats | Man page Source code |
| deIdentify | Man page Source code |
| detectionPnegEcdf | Man page Source code |
| diffRefSet | Man page Source code |
| dmContrasts | Man page Source code |
| dmr_combine_pval | Source code |
| dmr_merge_cpgs | Source code |
| dyeBiasCorr | Man page Source code |
| dyeBiasCorrMostBalanced | Man page Source code |
| dyeBiasCorrTypeINorm | Man page |
| dyeBiasL | Man page Source code |
| dyeBiasNL | Man page Source code |
| estimateLeukocyte | Man page Source code |
| exonToCDS | Source code |
| expand_url | Source code |
| formatVCF | Man page Source code |
| genotyper | Source code |
| getAFTypeIbySumAlleles | Man page Source code |
| getAFs | Man page Source code |
| getBetas | Man page Source code |
| getBinCoordinates | Man page Source code |
| getMask | Man page Source code |
| getRefSet | Man page Source code |
| getSignatureU | Source code |
| getSignatureUTop | Source code |
| guess_chrmorder | Source code |
| guess_dbnames | Source code |
| imputeBetas | Man page Source code |
| imputeBetasByGenomicNeighbors | Man page Source code |
| imputeBetasMatrixByMean | Man page Source code |
| inferEthnicity | Man page Source code |
| inferInfiniumIChannel | Man page Source code |
| inferPlatformFromTango | Source code |
| inferSex | Man page Source code |
| inferSpecies | Man page Source code |
| inferStrain | Man page Source code |
| inferTissue | Man page Source code |
| inferUniverse | Source code |
| initFileSet | Man page Source code |
| leftRightMerge1 | Source code |
| liftOver | Man page Source code |
| listAvailableMasks | Man page Source code |
| mLiftOver | Man page Source code |
| mapFileSet | Man page Source code |
| mapToMammal40 | Man page Source code |
| maskIG | Source code |
| match1To2_1state | Source code |
| match1To2_3states | Source code |
| matchDesign | Man page Source code |
| meanIntensity | Man page Source code |
| medianTotalIntensity | Man page Source code |
| model_contrasts | Source code |
| mouseBetaToAF | Source code |
| negControls | Man page Source code |
| noMasked | Man page Source code |
| nonuniqMask | Source code |
| noob | Man page Source code |
| noobSub | Source code |
| normControls | Man page Source code |
| normExpSignal | Source code |
| normalizeSetM | Source code |
| oobG | Source code |
| oobR | Source code |
| openSesame | Man page Source code |
| openSesameToFile | Man page Source code |
| pOOBAH | Man page Source code |
| palgen | Man page Source code |
| parseGEOsignalMU | Man page Source code |
| plotCytoBand | Source code |
| plotMapLines | Source code |
| plotTranscript1 | Source code |
| plotTranscripts | Source code |
| predictAge | Man page Source code |
| predictAgeHorvath353 | Man page Source code |
| predictAgeSkinBlood | Man page Source code |
| predictMouseAgeInMonth | Man page Source code |
| prefixMask | Man page Source code |
| prefixMaskButC | Man page Source code |
| prefixMaskButCG | Man page Source code |
| prepSesame | Man page Source code |
| prepSesameList | Man page Source code |
| preparePlotDF | Source code |
| print.DMLSummary | Man page Source code |
| print.fileSet | Man page Source code |
| probeID_designType | Man page Source code |
| probeSuccessRate | Man page Source code |
| qualityMask | Man page Source code |
| queryCheckPlatform | Source code |
| reIdentify | Man page Source code |
| readControls | Source code |
| readFileSet | Man page Source code |
| readIDAT | Source code |
| readIDAT1 | Source code |
| readIDAT_nonenc | Source code |
| readIDATpair | Man page Source code |
| recommendedMaskNames | Man page Source code |
| remove_suffix | Source code |
| resetMask | Man page Source code |
| scrub | Man page Source code |
| scrubSoft | Man page Source code |
| sdfMsg | Source code |
| sdfPlatform | Man page Source code |
| sdf_read_table | Man page Source code |
| sdf_write_table | Man page Source code |
| searchIDATprefixes | Man page Source code |
| segmentBins | Man page Source code |
| sesame | Man page |
| sesame-package | Man page |
| sesameAnno_attachManifest | Man page Source code |
| sesameAnno_buildAddressFile | Man page Source code |
| sesameAnno_buildManifestGRanges | Man page Source code |
| sesameAnno_download | Man page Source code |
| sesameAnno_readManifestTSV | Man page Source code |
| sesameQC-class | Man page |
| sesameQC_calcStats | Man page Source code |
| sesameQC_calcStats_betas | Source code |
| sesameQC_calcStats_channel | Source code |
| sesameQC_calcStats_detection | Source code |
| sesameQC_calcStats_dyeBias | Source code |
| sesameQC_calcStats_intensity | Source code |
| sesameQC_calcStats_numProbes | Source code |
| sesameQC_getStats | Man page Source code |
| sesameQC_plotBar | Man page Source code |
| sesameQC_plotBetaByDesign | Man page Source code |
| sesameQC_plotHeatSNPs | Man page Source code |
| sesameQC_plotIntensVsBetas | Man page Source code |
| sesameQC_plotRedGrnQQ | Man page Source code |
| sesameQC_rankStats | Man page Source code |
| sesameQCtoDF | Man page Source code |
| sesame_checkVersion | Man page Source code |
| sesamize | Man page Source code |
| setMask | Man page Source code |
| signalMU | Man page Source code |
| signalMU_oo | Source code |
| sliceFileSet | Man page Source code |
| speciesInfo | Source code |
| species_ret | Source code |
| subsetDBs | Source code |
| summaryExtractCf | Source code |
| summaryExtractTest | Man page Source code |
| testEnrichment | Man page Source code |
| testEnrichmentFisher | Man page Source code |
| testEnrichmentFisherN | Source code |
| testEnrichmentGene | Man page Source code |
| testEnrichmentSEA | Man page Source code |
| testEnrichmentSEA1 | Source code |
| testEnrichmentSpearman | Man page Source code |
| totalIntensities | Man page Source code |
| train.model.lm | Source code |
| twoCompsDiff | Source code |
| twoCompsEst2 | Man page Source code |
| updateSigDF | Man page Source code |
| valid_url | Source code |
| valleyDescent | Source code |
| vcf_header | Source code |
| visualizeGene | Man page Source code |
| visualizeProbes | Man page Source code |
| visualizeRegion | Man page Source code |
| visualizeSegments | Man page Source code |
| wrap_openSesame | Source code |
| wrap_openSesame1 | Source code |
