Files in zwdzwd/sesame

SEnsible Step-wise Analysis of DNA MEthylation BeadChips

LICENSE.md R/GEO.R R/KYCG.R R/KYCG_plot.R R/QC.R R/SigDFMethods.R R/age.R R/background.R R/cell_composition.R R/channel_inference.R R/cnv.R R/deidentify.R R/detection.R R/dm.R R/dye_bias.R R/ethnicity.R R/feature_selection.R R/fileSet.R R/impute.R R/mLiftOver.R R/mask.R R/match_design.R R/open.R R/palgen.R R/readIDAT.R R/sesame.R R/sesameAnno.R R/sex.R R/species.R R/strain.R R/tissue.R R/track.R R/utils.R R/vcf.R R/visualize.R R/visualizeHelper.R R/zzz.R README.md man/BetaValueToMValue.Rd man/DML.Rd man/DMLpredict.Rd man/DMR.Rd man/ELBAR.Rd man/KYCG_annoProbes.Rd man/KYCG_buildGeneDBs.Rd man/KYCG_getDBs.Rd man/KYCG_listDBGroups.Rd man/KYCG_loadDBs.Rd man/KYCG_plotBar.Rd man/KYCG_plotDot.Rd man/KYCG_plotEnrichAll.Rd man/KYCG_plotLollipop.Rd man/KYCG_plotManhattan.Rd man/KYCG_plotMeta.Rd man/KYCG_plotMetaEnrichment.Rd man/KYCG_plotPointRange.Rd man/KYCG_plotSetEnrichment.Rd man/KYCG_plotVolcano.Rd man/KYCG_plotWaterfall.Rd man/MValueToBetaValue.Rd man/SDFcollapseToPfx.Rd man/SigDF.Rd man/addMask.Rd man/aggregateTestEnrichments.Rd man/assemble_plots.Rd man/betasCollapseToPfx.Rd man/binSignals.Rd man/bisConversionControl.Rd man/calcEffectSize.Rd man/checkLevels.Rd man/chipAddressToSignal.Rd man/cnSegmentation.Rd man/compareDatbaseSetOverlap.Rd man/compareMouseStrainReference.Rd man/compareMouseTissueReference.Rd man/compareReference.Rd man/controls.Rd man/convertProbeID.Rd man/createDBNetwork.Rd man/createUCSCtrack.Rd man/dataFrame2sesameQC.Rd man/dbStats.Rd man/deidentify.Rd man/detectionPnegEcdf.Rd man/diffRefSet.Rd man/dmContrasts.Rd man/dyeBiasCorr.Rd man/dyeBiasCorrMostBalanced.Rd man/dyeBiasL.Rd man/dyeBiasNL.Rd man/estimateLeukocyte.Rd man/formatVCF.Rd man/getAFTypeIbySumAlleles.Rd man/getAFs.Rd man/getBetas.Rd man/getBinCoordinates.Rd man/getMask.Rd man/getRefSet.Rd man/imputeBetas.Rd man/imputeBetasByGenomicNeighbors.Rd man/imputeBetasMatrixByMean.Rd man/inferEthnicity.Rd man/inferInfiniumIChannel.Rd man/inferSex.Rd man/inferSpecies.Rd man/inferStrain.Rd man/inferTissue.Rd man/initFileSet.Rd man/liftOver.Rd man/listAvailableMasks.Rd man/mLiftOver.Rd man/mapFileSet.Rd man/mapToMammal40.Rd man/matchDesign.Rd man/meanIntensity.Rd man/medianTotalIntensity.Rd man/negControls.Rd man/noMasked.Rd man/noob.Rd man/normControls.Rd man/openSesame.Rd man/openSesameToFile.Rd man/pOOBAH.Rd man/palgen.Rd man/parseGEOsignalMU.Rd man/predictAge.Rd man/predictAgeHorvath353.Rd man/predictAgeSkinBlood.Rd man/predictMouseAgeInMonth.Rd man/prefixMask.Rd man/prefixMaskButC.Rd man/prefixMaskButCG.Rd man/prepSesame.Rd man/prepSesameList.Rd man/print.DMLSummary.Rd man/print.fileSet.Rd man/probeID_designType.Rd man/probeSuccessRate.Rd man/qualityMask.Rd man/reIdentify.Rd man/readFileSet.Rd man/readIDATpair.Rd man/recommendedMaskNames.Rd man/resetMask.Rd man/scrub.Rd man/scrubSoft.Rd man/sdfPlatform.Rd man/sdf_read_table.Rd man/sdf_write_table.Rd man/searchIDATprefixes.Rd man/segmentBins.Rd man/sesame-package.Rd man/sesameAnno_attachManifest.Rd man/sesameAnno_buildAddressFile.Rd man/sesameAnno_buildManifestGRanges.Rd man/sesameAnno_download.Rd man/sesameAnno_readManifestTSV.Rd man/sesameQC-class.Rd man/sesameQC_calcStats.Rd man/sesameQC_getStats.Rd man/sesameQC_plotBar.Rd man/sesameQC_plotBetaByDesign.Rd man/sesameQC_plotHeatSNPs.Rd man/sesameQC_plotIntensVsBetas.Rd man/sesameQC_plotRedGrnQQ.Rd man/sesameQC_rankStats.Rd man/sesameQCtoDF.Rd man/sesame_checkVersion.Rd man/sesamize.Rd man/setMask.Rd man/signalMU.Rd man/sliceFileSet.Rd man/summaryExtractTest.Rd man/testEnrichment.Rd man/testEnrichmentFisher.Rd man/testEnrichmentGene.Rd man/testEnrichmentSEA.Rd man/testEnrichmentSpearman.Rd man/totalIntensities.Rd man/twoCompsEst2.Rd man/updateSigDF.Rd man/visualizeGene.Rd man/visualizeProbes.Rd man/visualizeRegion.Rd man/visualizeSegments.Rd tests/testthat.R tests/testthat/test_detectionP.R tests/testthat/test_impute.R vignettes/KYCG.Rmd vignettes/QC.Rmd vignettes/inferences.Rmd vignettes/modeling.Rmd vignettes/nonhuman.Rmd vignettes/sesame.Rmd