Files in zwdzwd/sesame
SEnsible Step-wise Analysis of DNA MEthylation BeadChips
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS
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/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
inst/CITATION
inst/extdata/GSE36369_NonEBV_SignalA_SignalB_3samples_1k.txt.gz
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/estimateCellComposition.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/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_buildAddressFile.Rd
man/sesameAnno_buildManifestGRanges.Rd
man/sesameAnno_download.Rd
man/sesameAnno_get.Rd
man/sesameAnno_readManifestTSV.Rd
man/sesameData_getAnno.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/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/_output.yaml
vignettes/_site.yml
vignettes/include/after_body.html
vignettes/include/header.html
vignettes/include/logo.png
vignettes/include/site.css
vignettes/inferences.Rmd
vignettes/modeling.Rmd
vignettes/nonhuman.Rmd
vignettes/sesame.Rmd
