methylumi
Handle Illumina methylation data

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Functions
302
Source code
23
Man pages
21
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methylumi: Handle Illumina methylation data
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API

API for methylumi
Handle Illumina methylation data

Global functions
.combine.methylumiQC Source code
.combine.methylumiQC.27k.450k Source code
.combine.methylumiSets Source code
.doAssayDataNameSubstitutions Source code
.extractMethylationFdataAndAssayData Source code
.featureFilter Source code
.getFileSeparator Source code
.getFileType Source code
.getFinalReportBlock Source code
.getFinalReportHeader Source code
.getFinalReportMethylationProfile Source code
.mclapply Source code
.parallel Source code
.qcplot Source code
.readFinalReportMethylationFile Source code
.readOldMethylationFile Source code
.varFilter Source code
CSVtoDF Source code
CpGs Man page
Cy3.N Man page
Cy3.N,MethyLumiQC-method Man page
Cy3.N,MethyLumiSet-method Man page
Cy3<- Man page
Cy3<-,MethyLumiQC,matrix-method Man page
Cy5.N Man page
Cy5.N,MethyLumiQC-method Man page
Cy5.N,MethyLumiSet-method Man page
Cy5<- Man page
Cy5<-,MethyLumiQC,matrix-method Man page
DataToNChannelSet Source code
IDATsToDFs Man page
IDATsToMatrices Source code
IDATtoDF Man page
IDATtoMatrix Source code
MethyLumi-class Man page
MethyLumiM Man page
MethyLumiM-class Man page
MethyLumiQC-class Man page
MethyLumiSet-class Man page
NChannelSetToMethyLumiSet Man page Source code
QCdata Man page
QCdata,MethyLumiM-method Man page
QCdata,MethyLumiSet-method Man page
QCdata<- Man page
QCdata<-,MethyLumiSet Man page
QCdata<-,MethyLumiSet,MethyLumiQC-method Man page
SEtoGRset Source code
[,MethyLumiM,ANY-method Man page
[,MethyLumiSet,ANY-method Man page
beta.mme Source code
beta.mode Source code
beta.transform Source code
betas Man page
betas,GenomicMethylSet-method Man page
betas,MethyLumiM-method Man page
betas,MethyLumiSet-method Man page
betas,MethylSet-method Man page
betas,RangedSummarizedExperiment-method Man page
betas<- Man page
betas<-,MethyLumiSet,matrix-method Man page
boxplot,MethyLumiSet-method Man page
byChannel Source code
byChannel.Both Source code
byChannel.Grn Source code
byChannel.Red Source code
columnMatrix Source code
combine,MethyLumiM,MethyLumiM-method Man page
combine,MethyLumiQC,MethyLumiQC-method Man page
combine,MethyLumiSet,MethyLumiSet-method Man page
combine27k450k Man page
combine27k450k,MethyLumiSet,MethyLumiSet-method Man page
controlData Man page
controlData,MethyLumiM-method Man page
controlData,MethyLumiSet-method Man page
controlData<- Man page
controlData<-,MethyLumiM,ANY-method Man page
controlData<-,MethyLumiSet Man page
controlData<-,MethyLumiSet,MethyLumiQC-method Man page
controlTypes Man page
controlTypes,MethyLumiM-method Man page
controlTypes,MethyLumiQC-method Man page
controlTypes,MethyLumiSet-method Man page
corplot Man page
corplot,MethyLumiSet-method Man page
cy3 Man page Source code
cy5 Man page Source code
dataType Man page
dataType,MethyLumiM-method Man page
dataType<- Man page
dataType<-,MethyLumiM,ANY-method Man page
dataType<-,MethyLumiM-method Man page
designIItoMandU Man page Source code
designItoMandU Man page Source code
detection Man page
detection,MethyLumiM-method Man page
detection<- Man page
detection<-,MethyLumiM-method Man page
diagnostics Man page
diagnostics,methylData-method Man page
estimateM Man page Source code
exprs,MethyLumiSet-method Man page
extractAssayDataFromList Source code
extractBarcodeAndPosition Man page Source code
featureFilter Man page
featureFilter,MethyLumiM-method Man page
featureFilter,MethyLumiSet-method Man page
gamma.get.xcs Source code
gamma.get.xs Source code
gammaM.get.xcs Source code
gammaM.get.xs Source code
get.xcs Source code
get.xs Source code
getAssayDataNameSubstitutions Man page Source code
getBarcodes Man page Source code
getBiocPkgUrl Source code
getControlProbes Source code
getHistory Man page
getHistory,MethyLumiM-method Man page
getHistory,MethyLumiSet-method Man page
getMethylationBeadMappers Source code
getPlatform Source code
getProtocolData Man page
hist,MethyLumiQC-method Man page
hist,MethyLumiSet-method Man page
illumina.get.xcs Source code
illumina.get.xs Source code
intensities.IB Man page
intensities.IB,MethyLumiSet,character-method Man page
intensities.IB,MethyLumiSet,missing-method Man page
intensities.M Man page
intensities.M,MethyLumiSet,character-method Man page
intensities.M,MethyLumiSet,missing-method Man page
intensities.OOB Man page
intensities.OOB,MethyLumiSet,character-method Man page
intensities.OOB,MethyLumiSet,missing-method Man page
intensities.OOB.allelic Man page
intensities.OOB.allelic,MethyLumiSet,character,character-method Man page
intensities.OOB.allelic,MethyLumiSet,missing,missing-method Man page
intensities.U Man page
intensities.U,MethyLumiSet,character-method Man page
intensities.U,MethyLumiSet,missing-method Man page
intensitiesByChannel Man page
intensitiesByChannel,MethyLumiM-method Man page
intensitiesByChannel,MethyLumiQC-method Man page
intensitiesByChannel,MethyLumiSet-method Man page
lumIDAT Man page Source code
lumi.get.xcs Source code
lumi.get.xs Source code
lumiCSV Man page Source code
mOOB Source code
median.get.xcs Source code
median.get.xs Source code
mergeProbeDesigns Man page Source code
methylData-class Man page
methylated Man page
methylated,MethyLumi-method Man page
methylated,MethyLumiM-method Man page
methylated,MethyLumiQC-method Man page
methylated,MethyLumiSet-method Man page
methylated,MethylSet-method Man page
methylated.N Man page
methylated.N,MethyLumiM-method Man page
methylated.N,methylData-method Man page
methylated.N<- Man page
methylated.N<-,MethyLumiM,ANY-method Man page
methylated.N<-,methylData,matrix-method Man page
methylated<- Man page
methylated<-,MethyLumi,matrix-method Man page
methylated<-,MethyLumiM,ANY-method Man page
methylated<-,MethyLumiSet,matrix-method Man page
methylumIDAT Man page Source code
methylumi Man page
methylumi-package Man page
methylumi.bgcorr Man page Source code
methylumi.diagnostics Man page
methylumiCSV Man page Source code
methylumiR Man page Source code
methylumiToMinfi Source code
mldat Man page
mlumiToMset Source code
msetToSE Source code
myDensity Source code
negctls Man page
negctls,MethyLumiM,character-method Man page
negctls,MethyLumiM,missing-method Man page
negctls,MethyLumiQC,character-method Man page
negctls,MethyLumiQC,missing-method Man page
negctls,MethyLumiSet,character-method Man page
negctls,MethyLumiSet,missing-method Man page
negctls.stderr Man page
negctls.stderr,MethyLumiQC,character-method Man page
negctls.stderr,MethyLumiQC,missing-method Man page
negctls.stderr,MethyLumiSet,character-method Man page
negctls.stderr,MethyLumiSet,missing-method Man page
negnorm Man page
negnorm,MethyLumiM,character-method Man page
negnorm,MethyLumiM,missing-method Man page
negnorm,MethyLumiQC,character-method Man page
negnorm,MethyLumiQC,missing-method Man page
negnorm,MethyLumiSet,character-method Man page
negnorm,MethyLumiSet,missing-method Man page
normalizeMethyLumiSet Man page Source code
normalizeViaControls Source code
normctls Man page
normctls,MethyLumiM-method Man page
normctls,MethyLumiQC-method Man page
normctls,MethyLumiSet-method Man page
normexp.get.xcs Source code
normexp.get.xs Source code
pairs,MethyLumiSet-method Man page
plotNAs Man page
plotNAs,methylData-method Man page
plotNegOob Man page Source code
plotSampleIntensities Man page
plotSampleIntensities,MethyLumiSet-method Man page
pop Source code
probeNAs Man page
probeNAs,MethyLumiM-method Man page
probeNAs,MethyLumiSet-method Man page
psummary Man page
push Source code
pval.detect Man page
pval.detect,methylData-method Man page
pval.detect<- Man page
pval.detect<-,methylData,numeric-method Man page
pvals Man page
pvals,MethyLumi-method Man page
pvals,MethyLumiM-method Man page
pvals<- Man page
pvals<-,MethyLumi,matrix-method Man page
qc.probe.plot Man page Source code
qcplot Man page
qcplot,MethyLumiQC-method Man page
qcplot,MethyLumiSet-method Man page
qcplot,Methylumi-method Man page
readIDAT2 Source code
rowIQRs Source code
sampleNAs Man page
sampleNAs,MethyLumiM-method Man page
sampleNAs,MethyLumiSet-method Man page
sdmax Source code
shift Source code
show,MethyLumiSet-method Man page
stripBeadNs Man page Source code
stripBeadSDs Man page Source code
stripMethyLumiSet Man page Source code
stripOOB Man page Source code
summary,MethyLumi-method Man page
t.finish Source code Source code Source code
t.submit Source code Source code Source code
tcgaPipeline Source code
total.intensity Man page
total.intensity,MethyLumiM-method Man page
total.intensity,MethyLumiSet-method Man page
uOOB Source code
unmethylated Man page
unmethylated,MethyLumi-method Man page
unmethylated,MethyLumiM-method Man page
unmethylated,MethyLumiQC-method Man page
unmethylated,MethyLumiSet-method Man page
unmethylated,MethylSet-method Man page
unmethylated.N Man page
unmethylated.N,MethyLumiM-method Man page
unmethylated.N,methylData-method Man page
unmethylated.N<- Man page
unmethylated.N<-,MethyLumiM,ANY-method Man page
unmethylated.N<-,methylData,matrix-method Man page
unmethylated<- Man page
unmethylated<-,MethyLumi,matrix-method Man page
unmethylated<-,MethyLumiM,ANY-method Man page
unmethylated<-,MethyLumiSet,matrix-method Man page
unshift Source code
varFilter Man page
varFilter,MethyLumiM-method Man page
varFilter,MethyLumiSet-method Man page
methylumi documentation built on Nov. 8, 2020, 6:26 p.m.

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