Tools for HELP data analysis


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Documentation for package ‘HELP’ version 1.4.0

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B C E F G P Q R

-- B --

base.stacking.thermodynamics Base-stacking thermodynamic parameters

-- C --

calcGC Calculate GC percent
calcGC,character-method Calculate GC percent (methods)
calcGC,ExpressionSet-method Calculate GC percent (methods)
calcGC,missing-method Calculate GC percent (methods)
calcGC,NULL-method Calculate GC percent (methods)
calcGC-methods Calculate GC percent (methods)
calcPrototype Calculate prototype
calcPrototype,ExpressionSet-method Calculate prototype (methods)
calcPrototype,matrix-method Calculate prototype (methods)
calcPrototype,missing-method Calculate prototype (methods)
calcPrototype,vector-method Calculate prototype (methods)
calcPrototype-methods Calculate prototype (methods)
calcTm Calculate Tm
calcTm,character-method Calculate Tm (methods)
calcTm,ExpressionSet-method Calculate Tm (methods)
calcTm,missing-method Calculate Tm (methods)
calcTm,NULL-method Calculate Tm (methods)
calcTm-methods Calculate Tm (methods)
combineData Combine data
combineData,ExpressionSet,missing,missing-method Combine data (methods)
combineData,ExpressionSet,vector,missing-method Combine data (methods)
combineData,matrix,vector,matrix-method Combine data (methods)
combineData,matrix,vector,missing-method Combine data (methods)
combineData,missing,missing,missing-method Combine data (methods)
combineData,vector,missing,missing-method Combine data (methods)
combineData,vector,missing,vector-method Combine data (methods)
combineData,vector,vector,missing-method Combine data (methods)
combineData,vector,vector,vector-method Combine data (methods)
combineData-methods Combine data (methods)
createWiggle Create wiggle track
createWiggle,ExpressionSet,matrix-method Create wiggle track (methods)
createWiggle,ExpressionSet,missing-method Create wiggle track (methods)
createWiggle,matrix,matrix-method Create wiggle track (methods)
createWiggle,missing,missing-method Create wiggle track (methods)
createWiggle,vector,matrix-method Create wiggle track (methods)
createWiggle-methods Create wiggle track (methods)

-- E --

exprs2 Retrieve microarray data (for signal channel 2) from ExpressionSets
exprs2,ExpressionSet-method Retrieve microarray data (for signal channel 2) from ExpressionSets (methods)
exprs2,missing-method Retrieve microarray data (for signal channel 2) from ExpressionSets (methods)
exprs2-methods Retrieve microarray data (for signal channel 2) from ExpressionSets (methods)
exprs2<- Retrieve microarray data (for signal channel 2) from ExpressionSets
exprs2<-,ExpressionSet,matrix-method Retrieve microarray data (for signal channel 2) from ExpressionSets (methods)
exprs2<-,ExpressionSet,missing-method Retrieve microarray data (for signal channel 2) from ExpressionSets (methods)

-- F --

fuzzyMatches Fuzzy matching
fuzzyMatches,missing,missing-method Fuzzy matching (methods)
fuzzyMatches,NULL,vector-method Fuzzy matching (methods)
fuzzyMatches,vector,missing-method Fuzzy matching (methods)
fuzzyMatches,vector,NULL-method Fuzzy matching (methods)
fuzzyMatches,vector,vector-method Fuzzy matching (methods)
fuzzyMatches-methods Fuzzy matching (methods)

-- G --

getFeatures Get features (methods)
getFeatures,AnnotatedDataFrame,missing-method Get features (methods)
getFeatures,AnnotatedDataFrame,NULL-method Get features (methods)
getFeatures,AnnotatedDataFrame,vector-method Get features (methods)
getFeatures,ExpressionSet,missing-method Get features (methods)
getFeatures,ExpressionSet,NULL-method Get features (methods)
getFeatures,ExpressionSet,vector-method Get features (methods)
getFeatures,matrix,vector-method Get features (methods)
getFeatures,missing,missing-method Get features (methods)
getFeatures,vector,missing-method Get features (methods)
getFeatures,vector,NULL-method Get features (methods)
getFeatures,vector,vector-method Get features (methods)
getFeatures-methods Get features (methods)
getSamples Get samples
getSamples,ExpressionSet,missing-method Get samples (methods)
getSamples,ExpressionSet,NULL-method Get samples (methods)
getSamples,ExpressionSet,vector-method Get samples (methods)
getSamples,matrix,missing-method Get samples (methods)
getSamples,matrix,NULL-method Get samples (methods)
getSamples,matrix,vector-method Get samples (methods)
getSamples,missing,missing-method Get samples (methods)
getSamples,vector,missing-method Get samples (methods)
getSamples,vector,NULL-method Get samples (methods)
getSamples,vector,vector-method Get samples (methods)
getSamples-methods Get samples (methods)

-- P --

plotBins Plot bins
plotBins,ExpressionSet,ExpressionSet-method Plot bins (methods)
plotBins,ExpressionSet,missing-method Plot bins (methods)
plotBins,ExpressionSet,vector-method Plot bins (methods)
plotBins,matrix,missing-method Plot bins (methods)
plotBins,missing,missing-method Plot bins (methods)
plotBins,vector,ExpressionSet-method Plot bins (methods)
plotBins,vector,missing-method Plot bins (methods)
plotBins,vector,vector-method Plot bins (methods)
plotBins-methods Plot bins (methods)
plotChip Plot chip image
plotChip,ExpressionSet,ExpressionSet,missing-method Plot chip image (methods)
plotChip,ExpressionSet,missing,missing-method Plot chip image (methods)
plotChip,ExpressionSet,vector,missing-method Plot chip image (methods)
plotChip,matrix,missing,missing-method Plot chip image (methods)
plotChip,missing,missing,missing-method Plot chip image (methods)
plotChip,vector,vector,ExpressionSet-method Plot chip image (methods)
plotChip,vector,vector,vector-method Plot chip image (methods)
plotChip-methods Plot chip image (methods)
plotFeature Plot feature versus two-color intensity
plotFeature,ExpressionSet,missing-method Plot feature versus two-color intensity (methods)
plotFeature,ExpressionSet,vector-method Plot feature versus two-color intensity (methods)
plotFeature,matrix,vector-method Plot feature versus two-color intensity (methods)
plotFeature,missing,missing-method Plot feature versus two-color intensity (methods)
plotFeature-methods Plot feature versus two-color intensity (methods)
plotPairs Plot tree-pairs
plotPairs,ExpressionSet-method Plot tree-pairs (methods)
plotPairs,matrix-method Plot tree-pairs (methods)
plotPairs,missing-method Plot tree-pairs (methods)
plotPairs-methods Plot tree-pairs (methods)

-- Q --

quantileNormalize Quantile normalization
quantileNormalize,ExpressionSet,ExpressionSet-method Quantile normalization (methods)
quantileNormalize,ExpressionSet,missing-method Quantile normalization (methods)
quantileNormalize,ExpressionSet,vector-method Quantile normalization (methods)
quantileNormalize,matrix,missing-method Quantile normalization (methods)
quantileNormalize,missing,missing-method Quantile normalization (methods)
quantileNormalize,vector,ExpressionSet-method Quantile normalization (methods)
quantileNormalize,vector,missing-method Quantile normalization (methods)
quantileNormalize,vector,vector-method Quantile normalization (methods)
quantileNormalize-methods Quantile normalization (methods)

-- R --

readDesign Read NimbleGen design files
readDesign,character,character,character-method Read NimbleGen design files (methods)
readDesign,character,character,ExpressionSet-method Read NimbleGen design files (methods)
readDesign,missing,missing,missing-method Read NimbleGen design files (methods)
readDesign,vector,missing,missing-method Read NimbleGen design files (methods)
readDesign,vector,vector,missing-method Read NimbleGen design files (methods)
readDesign-methods Read NimbleGen design files (methods)
readPairs Read Nimblegen .pair files
readPairs,character,character,character-method Read Nimblegen .pair files (methods)
readPairs,character,character,ExpressionSet-method Read Nimblegen .pair files (methods)
readPairs,missing,missing,missing-method Read Nimblegen .pair files (methods)
readPairs,vector,missing,missing-method Read Nimblegen .pair files (methods)
readPairs,vector,vector,missing-method Read Nimblegen .pair files (methods)
readPairs-methods Read Nimblegen .pair files (methods)
readSampleKey Read sample key