# Reverse-Phase Protein Array Super Position and Concentration Evaluation

## Documentation for package ‘RPPASPACE’ version 1.0.7

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

C D F G H I L N P Q R S T W

RPPASPACE-package | Reverse phase protein lysate array analysis

## -- C --

CobsFitClass-class | Class "CobsFitClass"
coef-method | Class "RPPAFit"
coef-method | Class "FitClass"
coef-method | Class "LogisticFitClass"
coefficients-method | Class "RPPAFit"
coefficients-method | Class "FitClass"
coefficients-method | Class "LogisticFitClass"
coerce-method | Class "Directory"

## -- D --

dim-method | Class "RPPA"
Directory | Class "Directory"
Directory-class | Class "Directory"
DS5RPPAPreFitQC-class | Class "DS5RPPAPreFitQC"

## -- F --

FitClass-class | Class "FitClass"
fitCurveAndSummarizeFromSettings | Class "RPPASPACESettings"
fitSeries-method | Class "FitClass"
fitSeries-method | Class "LogisticFitClass"
fitSeries-method | Class "CobsFitClass"
fitSeries-method | Class "LoessFitClass"
fitSlide-method | Class "FitClass"
fitSlide-method | Class "LogisticFitClass"
fitSlide-method | Class "CobsFitClass"
fitSlide-method | Class "LoessFitClass"
fitted-method | Class "RPPAFit"
fitted-method | Class "FitClass"
fitted-method | Class "LogisticFitClass"
fitted-method | Class "CobsFitClass"
fitted-method | Class "LoessFitClass"

## -- G --

getConfidenceInterval | Compute Confidence Intervals for a Model Fit to Dilution Series
getRegisteredModel | Model Registration Methods
getRegisteredModelKeys | Model Registration Methods
getRegisteredModelLabel | Model Registration Methods
getRegisteredNormalizationMethod | Normalization Method Registration Methods
getRegisteredNormalizationMethodKeys | Normalization Method Registration Methods
getRegisteredNormalizationMethodLabel | Normalization Method Registration Methods

## -- H --

hist-method | Class "RPPAFit"

## -- I --

image-method | Class "RPPA"
image-method | Class "RPPAFit"
is.Directory | Class "Directory"
is.FitClass | Class "FitClass"
is.RPPA | Class "RPPA"
is.RPPADesignParams | Class "RPPADesignParams"
is.RPPAFit | Fitting Dilution Curves to Protein Lysate Arrays with Class "RPPAFitParams"
is.RPPAFitParams | Fitting Dilution Curves to Protein Lysate Arrays with Class "RPPAFitParams"
is.RPPANormalizationParams | Class "RPPANormalizationParams"
is.RPPAPreFitQC | Class "RPPAPreFitQC"
is.RPPASet | Class "RPPASet"
is.RPPASetSummary | Class "RPPASetSummary"
is.RPPASPACESettings | Class "RPPASPACESettings"
is.RPPASpatialParams | Class "RPPASpatialParams"

## -- L --

LoessFitClass-class | Class "LoessFitClass"
LogisticFitClass-class | Class "LogisticFitClass"

## -- N --

normalize | Method "normalize"
normalize-method | Class "RPPASet"
normalize-method | Normalization
normalize-method | Method "normalize"

## -- P --

paramString-method | Class "RPPADesignParams"
paramString-method | Fitting Dilution Curves to Protein Lysate Arrays with Class "RPPAFitParams"
paramString-method | Class "RPPANormalizationParams"
paramString-method | Class "RPPASpatialParams"
paramString-method | Class "RPPASPACESettings"
plot-method | Class "RPPA"
plot-method | Class "RPPADesignParams"
plot-method | Class "RPPAFit"

## -- Q --

qcprob | Method "qcprob"
qcprob-method | Class "RPPAPreFitQC"
qcprob-method | Class "DS5RPPAPreFitQC"
qcprob-method | Method "qcprob"

## -- R --

registerModel | Model Registration Methods
registerNormalizationMethod | Normalization Method Registration Methods
resid-method | Class "RPPAFit"
residuals-method | Class "RPPAFit"
RPPA | Class "RPPA"
RPPA-class | Class "RPPA"
RPPADesignParams | Class "RPPADesignParams"
RPPADesignParams-class | Class "RPPADesignParams"
RPPAFit | Fitting Dilution Curves to Protein Lysate Arrays with Class "RPPAFitParams"
RPPAFit-class | Class "RPPAFit"
RPPAFitFromParams | Fitting Dilution Curves to Protein Lysate Arrays with Class "RPPAFitParams"
RPPAFitParams | Fitting Dilution Curves to Protein Lysate Arrays with Class "RPPAFitParams"
RPPAFitParams-class | Fitting Dilution Curves to Protein Lysate Arrays with Class "RPPAFitParams"
RPPANormalizationParams | Class "RPPANormalizationParams"
RPPANormalizationParams-class | Class "RPPANormalizationParams"
RPPAPreFitQC | Class "RPPAPreFitQC"
RPPAPreFitQC-class | Class "RPPAPreFitQC"
RPPASet | Class "RPPASet"
RPPASet-class | Class "RPPASet"
RPPASetSummary | Class "RPPASetSummary"
RPPASetSummary-class | Class "RPPASetSummary"
RPPASPACESettings | Class "RPPASPACESettings"
RPPASPACESettings-class | Class "RPPASPACESettings"
RPPASpatialParams | Class "RPPASpatialParams"
RPPASpatialParams-class | Class "RPPASpatialParams"

## -- S --

seriesNames | Class "RPPA"
seriesToUseToMakeCurve | Class "RPPA"
spatialAdjustment | Spatial Correction
spatialAdjustmentFromParams | Spatial Correction
spatialCorrection | Spatial Correction
summary-method | Class "RPPA"
summary-method | Class "RPPAFit"
summary-method | Class "RPPASet"
summary-method | Class "RPPAPreFitQC"
summary-method | Class "DS5RPPAPreFitQC"

## -- T --

trimConc-method | Class "FitClass"
trimConc-method | Class "LogisticFitClass"
trimConc-method | Class "CobsFitClass"
trimConc-method | Class "LoessFitClass"

## -- W --

write.summary | Method "write.summary"
write.summary-method | Class "RPPASet"
write.summary-method | Class "RPPASetSummary"
write.summary-method | Class "RPPASPACESettings"
write.summary-method | Method "write.summary"