API for zwdzwd/sesame
SEnsible Step-wise Analysis of DNA MEthylation BeadChips

Global functions
.backgroundCorrCh1 Source code
.onAttach Source code
.optimizeCellComposition 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
dichotomize Source code
diffRefSet Man page Source code
dmContrasts Man page Source code
dmr_combine_pval Source code
dmr_merge_cpgs Source code
double.transform.f 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
errFunc Source code
estimateCellComposition 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
getg0 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
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
zwdzwd/sesame documentation built on June 24, 2024, 6:34 p.m.