# Tools for HELP data analysis

## Documentation for package ‘HELP’ version 1.2.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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