Global functions | |
---|---|
ArrayWeights | Man page |
ArrayWeights,limmaResults-method | Man page |
ArrayWeights<- | Man page |
ArrayWeights<-,limmaResults,numeric-method | Man page |
BASH | Man page |
BASHCompact | Man page |
BASHDiffuse | Man page |
BASHExtended | Man page |
BeadLevelList | Man page |
BeadLevelList-class | Man page |
ContrastMatrix | Man page |
ContrastMatrix,limmaResults-method | Man page |
ContrastMatrix<- | Man page |
ContrastMatrix<-,limmaResults,matrix-method | Man page |
DesignMatrix | Man page |
DesignMatrix,limmaResults-method | Man page |
DesignMatrix<- | Man page |
DesignMatrix<-,limmaResults,matrix-method | Man page |
Detection | Man page |
Detection,ExpressionSetIllumina-method | Man page |
Detection<- | Man page |
Detection<-,ExpressionSetIllumina,matrix-method | Man page |
ExpressionSetIllumina-class | Man page |
HULK | Man page |
LogFC | Man page |
LogFC,limmaResults-method | Man page |
LogFC<- | Man page |
LogFC<-,limmaResults,matrix-method | Man page |
LogOdds | Man page |
LogOdds,limmaResults-method | Man page |
LogOdds<- | Man page |
LogOdds<-,limmaResults,matrix-method | Man page |
PValue | Man page |
PValue,limmaResults-method | Man page |
PValue<- | Man page |
PValue<-,limmaResults,matrix-method | Man page |
[,ExpressionSetIllumina,ANY-method | Man page |
[,ExpressionSetIllumina-method | Man page |
[,limmaResults-method | Man page |
[[,beadLevelData,ANY,missing-method | Man page |
addFeatureData | Man page |
annotation | Man page |
annotation,ExpressionSetIllumina-method | Man page |
annotation,beadLevelData-method | Man page |
annotation<-,ExpressionSetIllumina,character-method | Man page |
annotation<-,beadLevelData,character-method | Man page |
arrayNames | Man page |
arrayNames,BeadLevelList-method | Man page |
backgroundCorrectSingleSection | Man page |
beadLevelData-class | Man page |
beadRegistrationData-class | Man page |
beadStatusVector | Man page |
beadarray-package | Man page |
beadarrayUsersGuide | Man page |
boxplot,ExpressionSetIllumina-method | Man page |
boxplot,beadLevelData-method | Man page |
boxplot,beadRegistrationData-method | Man page |
calculateDetection | Man page |
calculateOutlierStats | Man page |
checkPlatform | Man page |
checkRegistration | Man page |
combine,ExpressionSetIllumina,ExpressionSetIllumina-method | Man page Man page |
combine,beadLevelData,beadLevelData-method | Man page |
combine,limmaResults,limmaResults-method | Man page |
combinedControlPlot | Man page |
controlProbeDetection | Man page |
convertBeadLevelList | Man page |
createBeadSummaryData | Man page |
createGEOMatrix | Man page |
createGEOMeta | Man page |
createTargetsFile | Man page |
dim,ExpressionSetIllumina-method | Man page |
dim,beadLevelData-method | Man page |
dim,limmaResults-method | Man page |
expressionQCPipeline | Man page |
exprs,ExpressionSetIllumina-method | Man page |
exprs<-,ExpressionSetIllumina,matrix-method | Man page |
generateNeighbours | Man page |
genericBeadIntensityPlot | Man page |
getAnnotation | Man page |
getArrayData | Man page |
getArrayData,BeadLevelList-method | Man page |
getBeadData | Man page |
getControlProfile | Man page |
greenChannel | Man page |
greenChannelTransform | Man page |
identifyControlBeads | Man page |
illuminaBackground | Man page |
illuminaChannel-class | Man page |
illuminaForeground | Man page |
illuminaOutlierMethod | Man page |
illuminaSharpen | Man page |
imageplot | Man page |
insertBeadData | Man page |
insertSectionData | Man page |
limmaDE | Man page |
limmaResults-class | Man page |
logGreenChannelTransform | Man page |
logRatioTransform | Man page |
logRedChannelTransform | Man page |
makeControlProfile | Man page |
makeGEOSubmissionFiles | Man page |
makeQCTable | Man page |
medianBackground | Man page |
medianNormalise | Man page |
metaTemplate | Man page |
metrics | Man page |
metrics,beadLevelData-method | Man page |
nObservations | Man page |
nObservations,ExpressionSetIllumina-method | Man page |
nObservations<- | Man page |
nObservations<-,ExpressionSetIllumina,matrix-method | Man page |
noOutlierMethod | Man page |
normaliseIllumina | Man page |
numBeads | Man page |
numBeads,beadLevelData-method | Man page |
outlierplot | Man page |
p95 | Man page |
p95,beadLevelData,character-method | Man page |
platformSigs | Man page |
plot,limmaResults-method | Man page |
plotBeadIntensities | Man page |
plotBeadLocations | Man page |
plotChipLayout | Man page |
plotMA | Man page |
plotMA,ExpressionSetIllumina-method | Man page |
plotMAXY | Man page |
plotTIFF | Man page |
plotXY | Man page |
poscontPlot | Man page |
processSwathData | Man page |
qcData | Man page |
qcData,ExpressionSetIllumina-method | Man page |
quickSummary | Man page |
readBeadSummaryData | Man page |
readIdatFiles | Man page |
readIllumina | Man page |
readLocsFile | Man page |
readSampleSheet | Man page |
readTIFF | Man page |
redChannelTransform | Man page |
removeBeadData | Man page |
sampleSheet | Man page |
sampleSheet,ExpressionSetIllumina-method | Man page |
sampleSheet,beadLevelData-method | Man page |
sampleSheet<- | Man page |
sampleSheet<-,ExpressionSetIllumina,data.frame-method | Man page |
sampleSheet<-,beadLevelData,data.frame-method | Man page |
se.exprs,ExpressionSetIllumina-method | Man page |
se.exprs<-,ExpressionSetIllumina,matrix-method | Man page |
sectionNames | Man page |
sectionNames,beadLevelData-method | Man page |
setAnnotation | Man page |
setWeights | Man page |
show,ExpressionSetIllumina-method | Man page |
show,beadLevelData-method | Man page |
show,beadRegistrationData-method | Man page |
show,limmaResults-method | Man page |
showArrayMask | Man page |
snr | Man page |
snr,beadLevelData,character-method | Man page |
squeezedVarOutlierMethod | Man page |
suggestAnnotation | Man page |
summarize | Man page |
weightsOutlierMethod | Man page |
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