SuperCurve: RPPA Analysis Package
Version 1.5.15

Analyze reverse phase protein lysate arrays.

Browse man pages Browse package API and functions Browse package files

AuthorKevin R. Coombes, Shannon Neeley, Corwin Joy, Jianhua Hu, Keith Baggerly, and P. Roebuck
Date of publication2017-04-28 12:31:40
Maintainer"P. Roebuck" <proebuck@mdanderson.org>
LicenseArtistic-2.0
Version1.5.15
URL http://r-forge.r-project.org/projects/supercurve/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SuperCurve", repos="http://R-Forge.R-project.org")

Man pages

sc00-SuperCurve-package: Reverse phase protein lysate array analysis
sc01-RPPA-class: Class "RPPA"
sc02-RPPADesign-class: Class "RPPADesign" and Class "RPPADesignParams"
sc05-RPPAFit-class: Class "RPPAFit"
sc06-RPPAFitParams-class: Fitting Dilution Curves to Protein Lysate Arrays with Class...
sc07-FitClass-class: Class "FitClass"
sc08-LogisticFitClass-class: Class "LogisticFitClass"
sc09-CobsFitClass-class: Class "CobsFitClass"
sc10-LoessFitClass-class: Class "LoessFitClass"
sc11-RPPASet-class: Class "RPPASet"
sc12-RPPASetSummary-class: Class "RPPASetSummary"
sc13-getConfidenceInterval: Compute Confidence Intervals for a Model Fit to Dilution...
sc14-spatialCorrection: Spatial Correction
sc15-normalize: Normalization
sc19-RPPANormalizationParams-class: Class "RPPANormalizationParams"
sc20-RPPASpatialParams-class: Class "RPPASpatialParams"
sc21-RPPAPreFitQC-class: Class "RPPAPreFitQC"
sc22-DS5RPPAPreFitQC-class: Class "DS5RPPAPreFitQC"
sc70-rppaCell-data: AKT, ERK2, and CTNNB1 expression in cell lines
sc70-rppaSingleSubgrid-data: FOO, BAR, PLUGH, and WALDO expression
sc70-rppaTriple-data: ACTB, CAS3, FAK, and ODC1 expression in 14 fed/starved cell...
sc70-rppaTumor-data: ERK2, GSK3, and JNK expression in tumor samples
sc80-registerModel: Model Registration Methods
sc80-registerNormalizationMethod: Normalization Method Registration Methods
sc90-registrationMethods: Generic Registration Methods
sc98-BoundedRange-class: Class "BoundedRange"
sc98-DefaultProgressMonitor-class: Class "DefaultProgressMonitor"
sc98-Directory-class: Class "Directory"
sc98-ElapsedTime-class: Class "ElapsedTime"
sc98-ProgressMonitor-class: Class "ProgressMonitor"
sc98-ProgressMonitor-methods: Methods for Manipulating Progress Monitors
sc98-SCProgressMonitor-class: Class "SCProgressMonitor"
sc98-SCProgressMonitor-methods: Methods for Manipulating SuperCurve Progress Models
sc98-SuperCurveSettings-class: Class "SuperCurveSettings"
sc99-elapsed-method: Method "elapsed"
sc99-normalize-method: Method "normalize"
sc99-paramString-method: Method "paramString"
sc99-qcprob-method: Method "qcprob"
sc99-write.summary-method: Method "write.summary"

Functions

BoundedRange Man page Source code
BoundedRange-class Man page
CobsFitClass-class Man page
DS5RPPAPreFitQC Source code
DS5RPPAPreFitQC-class Man page
DefaultProgressMonitor Man page Source code
DefaultProgressMonitor-class Man page
Directory Man page Source code
Directory-class Man page
ElapsedTime Man page Source code
ElapsedTime-class Man page
FitClass-class Man page
LoessFitClass-class Man page
LogisticFitClass-class Man page
ProgressMonitor-class Man page
RPPA Man page Source code
RPPA-class Man page
RPPADesign Man page Source code
RPPADesign-class Man page
RPPADesignFromParams Man page Source code
RPPADesignParams Man page Source code
RPPADesignParams-class Man page
RPPAFit Man page Source code
RPPAFit-class Man page
RPPAFitFromParams Man page Source code
RPPAFitParams Man page Source code
RPPAFitParams-class Man page
RPPANormalizationParams Man page Source code
RPPANormalizationParams-class Man page
RPPAPreFitQC Man page Source code
RPPAPreFitQC-class Man page
RPPASet Man page Source code
RPPASet-class Man page
RPPASetSummary Man page Source code
RPPASetSummary-class Man page
RPPASpatialParams Man page Source code
RPPASpatialParams-class Man page
SCProgressMonitor Man page Source code
SCProgressMonitor-class Man page
SuperCurve-package Man page
SuperCurveSettings Man page Source code
SuperCurveSettings-class Man page
actb Man page
actb.gray Man page
akt Man page
bar Man page
c.erk2 Man page
calcLogitz Source code
capwords Source code
cas3 Man page
coef,FitClass-method Man page
coef,LogisticFitClass-method Man page
coef,RPPAFit-method Man page
coef.quantile.est Source code
coefficients,FitClass-method Man page
coefficients,LogisticFitClass-method Man page
coefficients,RPPAFit-method Man page
coerce,Directory,character-method Man page
coerce,character,Directory-method Man page
computeBackgroundCutoff Source code
controlVector Source code
createFitGraphs Source code
ctnnb1 Man page
design40 Man page
dim,RPPA-method Man page
dim,RPPADesign-method Man page
dimOfLayout Source code
dir.exists Source code
dir.writable Source code
ea Source code
elapsed Man page
elapsed,ANY-method Man page
elapsed,DefaultProgressMonitor-method Man page
elapsed,ElapsedTime-method Man page
elapsed-method Man page
erk2 Man page
est.bg.noise Source code
fak Man page
firstPass Source code
fitColnames Source code
fitCurveAndSummarizeFromSettings Man page Source code
fitSeries,CobsFitClass-method Man page
fitSeries,FitClass-method Man page
fitSeries,LoessFitClass-method Man page
fitSeries,LogisticFitClass-method Man page
fitSlide,CobsFitClass-method Man page
fitSlide,FitClass-method Man page
fitSlide,LoessFitClass-method Man page
fitSlide,LogisticFitClass-method Man page
fitSlot Source code
fitted,CobsFitClass-method Man page
fitted,FitClass-method Man page
fitted,LoessFitClass-method Man page
fitted,LogisticFitClass-method Man page
fitted,RPPAFit-method Man page
foo Man page
generic.trim Source code
getConfidenceInterval Man page Source code
getLayoutMethod Source code
getPrerequisitePackages Source code
getReadMethod Source code
getRegisteredMethod Man page Source code
getRegisteredMethodKeys Man page
getRegisteredModel Man page Source code
getRegisteredModelKeys Man page Source code
getRegisteredModelLabel Man page Source code
getRegisteredNormalizationMethod Man page Source code
getRegisteredNormalizationMethodKeys Man page Source code
getRegisteredNormalizationMethodLabel Man page Source code
getRegisteredObject Man page Source code
getRegisteredObjectKeys Man page Source code
getStages Man page Source code
getSteps Man page Source code
gsk3 Man page
hasScheme Source code
hist,RPPAFit-method Man page
image,RPPA-method Man page
image,RPPADesign-method Man page
image,RPPAFit-method Man page
is.BoundedRange Man page Source code
is.DefaultProgressMonitor Man page
is.Directory Man page Source code
is.ElapsedTime Man page Source code
is.FitClass Man page Source code
is.ProgressMonitor Man page Source code
is.RPPA Man page Source code
is.RPPADesign Man page Source code
is.RPPADesignParams Man page Source code
is.RPPAFit Man page Source code
is.RPPAFitParams Man page Source code
is.RPPANormalizationParams Man page Source code
is.RPPAPreFitQC Man page Source code
is.RPPASet Man page Source code
is.RPPASetSummary Man page Source code
is.RPPASpatialParams Man page Source code
is.SCProgressMonitor Man page Source code
is.SuperCurveSettings Man page Source code
jnk Man page
layout Source code
layout.as.superslide Source code
loadAntibodyInfo Source code
locationColnames Source code
loess.line Source code
mergeDataWithLayout Source code
mergeGraphsAndImage Source code
mkDefaultMethod Source code
mkDefaultReplaceMethod Source code
mkNumericHandlerMethod Source code
mkPlotTitle Source code
modelenv Source code
names,RPPADesign-method Man page
normalize Man page
normalize,ANY-method Man page
normalize,MatrixLike-method Man page
normalize,NULL-method Man page
normalize,RPPASet-method Man page
normalize-method Man page
normalize.house Source code
normalize.median Source code
normalize.medpolish Source code
normalize.vs Source code
normenv Source code
odc1 Man page
onAttach Source code
onLoad Source code
packaged Source code
paramString Man page
paramString,ANY-method Man page
paramString,RPPADesignParams-method Man page
paramString,RPPAFitParams-method Man page
paramString,RPPANormalizationParams-method Man page
paramString,RPPASpatialParams-method Man page
paramString,SuperCurveSettings-method Man page
paramString-method Man page
pathname Source code
pkgRversion Source code
plot,RPPA,RPPADesign-method Man page
plot,RPPAFit,missing-method Man page
plotProbabilityOfGoodSlide Source code
plugh Man page
portableFilename Source code
predict.spline Source code
progressDone Man page
progressDone,ANY-method Man page
progressDone,DefaultProgressMonitor-method Man page
progressDone,ProgressMonitor-method Man page
progressDone-method Man page
progressDone<- Man page
progressDone<-,ANY,ANY-method Man page
progressDone<-,DefaultProgressMonitor,logical-method Man page
progressDone<-,ProgressMonitor,ANY-method Man page
progressDone<--method Man page
progressError Man page
progressError,ANY-method Man page
progressError,DefaultProgressMonitor-method Man page
progressError,ProgressMonitor-method Man page
progressError-method Man page
progressError<- Man page
progressError<-,ANY,ANY-method Man page
progressError<-,DefaultProgressMonitor,logical-method Man page
progressError<-,ProgressMonitor,ANY-method Man page
progressError<--method Man page
progressLabel Man page
progressLabel,ANY-method Man page
progressLabel,DefaultProgressMonitor-method Man page
progressLabel,ProgressMonitor-method Man page
progressLabel-method Man page
progressLabel<- Man page
progressLabel<-,ANY,ANY-method Man page
progressLabel<-,DefaultProgressMonitor,character-method Man page
progressLabel<-,ProgressMonitor,ANY-method Man page
progressLabel<--method Man page
progressMarquee Man page
progressMarquee,ANY-method Man page
progressMarquee,SCProgressMonitor-method Man page
progressMarquee-method Man page
progressMarquee<- Man page
progressMarquee<-,ANY-method Man page
progressMarquee<-,SCProgressMonitor,character-method Man page
progressMarquee<--method Man page
progressMaximum Man page
progressMaximum,ANY-method Man page
progressMaximum,BoundedRange-method Man page
progressMaximum,DefaultProgressMonitor-method Man page
progressMaximum,ProgressMonitor-method Man page
progressMaximum-method Man page
progressMaximum<- Man page
progressMaximum<-,ANY,ANY-method Man page
progressMaximum<-,BoundedRange,numeric-method Man page
progressMaximum<-,DefaultProgressMonitor,numeric-method Man page
progressMaximum<-,ProgressMonitor,ANY-method Man page
progressMaximum<--method Man page
progressMinimum Man page
progressMinimum,ANY-method Man page
progressMinimum,BoundedRange-method Man page
progressMinimum,DefaultProgressMonitor-method Man page
progressMinimum,ProgressMonitor-method Man page
progressMinimum-method Man page
progressMinimum<- Man page
progressMinimum<-,ANY,ANY-method Man page
progressMinimum<-,BoundedRange,numeric-method Man page
progressMinimum<-,DefaultProgressMonitor,numeric-method Man page
progressMinimum<-,ProgressMonitor,ANY-method Man page
progressMinimum<--method Man page
progressStage Man page
progressStage,ANY-method Man page
progressStage,SCProgressMonitor-method Man page
progressStage-method Man page
progressStage<- Man page
progressStage<-,ANY-method Man page
progressStage<-,SCProgressMonitor,character-method Man page
progressStage<--method Man page
progressValue Man page
progressValue,ANY-method Man page
progressValue,BoundedRange-method Man page
progressValue,DefaultProgressMonitor-method Man page
progressValue,ProgressMonitor-method Man page
progressValue-method Man page
progressValue<- Man page
progressValue<-,ANY,ANY-method Man page
progressValue<-,BoundedRange,numeric-method Man page
progressValue<-,DefaultProgressMonitor,numeric-method Man page
progressValue<-,ProgressMonitor,ANY-method Man page
progressValue<--method Man page
qcprob Man page
qcprob,ANY-method Man page
qcprob,DS5RPPAPreFitQC-method Man page
qcprob,NULL-method Man page
qcprob,RPPAPreFitQC-method Man page
qcprob-method Man page
ran.prefitqc Source code
read.arraypro Source code
read.microvigene Source code
readQuantification Source code
registerClassname Man page Source code
registerMethod Man page Source code
registerModel Man page Source code
registerNormalizationMethod Man page Source code
registerPkgFitModels Source code
registerPkgNormalizationMethods Source code
resid,RPPAFit-method Man page
residuals,RPPAFit-method Man page
rppaCell Man page
rppaCell-data Man page
rppaNormalize Source code
rppaSingleSubgrid Man page
rppaSingleSubgrid-data Man page
rppaTriple Man page
rppaTriple-data Man page
rppaTumor Man page
rppaTumor-data Man page
sAbsolutePathname Source code
sPackageInstalled Source code
sProbability Source code
sdesign Man page
series.fit Source code
seriesNames Man page Source code
slide.model Source code
slot.all.equal Source code
software Source code
spatialAdjustment Man page Source code
spatialAdjustmentFromParams Man page Source code
spatialCorrection Man page Source code
summary,DS5RPPAPreFitQC-method Man page
summary,RPPA-method Man page
summary,RPPADesign-method Man page
summary,RPPAFit-method Man page
summary,RPPAPreFitQC-method Man page
summary,RPPASet-method Man page
tDesign Man page
totitle Source code
trimConc,CobsFitClass-method Man page
trimConc,FitClass-method Man page
trimConc,LoessFitClass-method Man page
trimConc,LogisticFitClass-method Man page
tripledesign Man page
validBoundedRange Source code
validDirectory Source code
validRPPADesign Source code
validRPPANormalizationParams Source code
validSpatialParams Source code
validSuperCurveSettings Source code
validate.classname Source code
validate.envir Source code
validate.key Source code
validate.method Source code
waldo Man page
write.summary Man page
write.summary,ANY-method Man page
write.summary,RPPASet-method Man page
write.summary,RPPASetSummary-method Man page
write.summary,SuperCurveSettings-method Man page
write.summary-method Man page

Files

.aspell
.aspell/defaults.R
.aspell/en-antibodies.rds
.aspell/en-developer.rds
.aspell/en-microarray.rds
.aspell/en-software.rds
.aspell/en-statistics.rds
DESCRIPTION
NAMESPACE
NEWS
R
R/AllElapsedTimeGenerics.R
R/AllGenerics.R
R/AllProgressMonitorGenerics.R
R/AllSCProgressMonitorGenerics.R
R/BoundedRange.R
R/Directory-class.R
R/ElapsedTime.R
R/NULL-methods.R
R/ProgressMonitor.R
R/SCProgressMonitor.R
R/bisection.search.R
R/readQuantification.R
R/registration.R
R/sc1-rppa.R
R/sc2-design.R
R/sc3-0-dilutionFitMethods.R
R/sc3-1-dilutionFit.R
R/sc3-2-mainFit.R
R/sc4-normalize.R
R/sc4-spatial.R
R/sc5-rppaSet.R
R/sc6-rppaSetSummary.R
R/sc8-prefitqc.R
R/sc98-settings.R
R/sc99-fitcurve.R
R/utils.R
R/zzz.R
build
build/SuperCurve.pdf
build/vignette.rds
data
data/rppaCell.RData
data/rppaSingleSubgrid.RData
data/rppaTriple.RData
data/rppaTumor.RData
inst
inst/COPYRIGHTS
inst/doc
inst/doc/SuperCurve.R
inst/doc/SuperCurve.Rnw
inst/doc/SuperCurve.pdf
inst/images
inst/images/missing_slide.tif
inst/sampleCode
inst/sampleCode/simExample.R
inst/sampleCode/supercurveSettings.R
inst/sampleCode/zz-examples.R
inst/util
inst/util/mkRPPACellDataset.R
inst/util/mkRPPASingleSubgridDataset.R
inst/util/mkRPPATripleDataset.R
inst/util/mkRPPATumorDataset.R
man
man/sc00-SuperCurve-package.Rd
man/sc01-RPPA-class.Rd
man/sc02-RPPADesign-class.Rd
man/sc05-RPPAFit-class.Rd
man/sc06-RPPAFitParams-class.Rd
man/sc07-FitClass-class.Rd
man/sc08-LogisticFitClass-class.Rd
man/sc09-CobsFitClass-class.Rd
man/sc10-LoessFitClass-class.Rd
man/sc11-RPPASet-class.Rd
man/sc12-RPPASetSummary-class.Rd
man/sc13-getConfidenceInterval.Rd
man/sc14-spatialCorrection.Rd
man/sc15-normalize.Rd
man/sc19-RPPANormalizationParams-class.Rd
man/sc20-RPPASpatialParams-class.Rd
man/sc21-RPPAPreFitQC-class.Rd
man/sc22-DS5RPPAPreFitQC-class.Rd
man/sc70-rppaCell-data.Rd
man/sc70-rppaSingleSubgrid-data.Rd
man/sc70-rppaTriple-data.Rd
man/sc70-rppaTumor-data.Rd
man/sc80-registerModel.Rd
man/sc80-registerNormalizationMethod.Rd
man/sc90-registrationMethods.Rd
man/sc98-BoundedRange-class.Rd
man/sc98-DefaultProgressMonitor-class.Rd
man/sc98-Directory-class.Rd
man/sc98-ElapsedTime-class.Rd
man/sc98-ProgressMonitor-class.Rd
man/sc98-ProgressMonitor-methods.Rd
man/sc98-SCProgressMonitor-class.Rd
man/sc98-SCProgressMonitor-methods.Rd
man/sc98-SuperCurveSettings-class.Rd
man/sc99-elapsed-method.Rd
man/sc99-normalize-method.Rd
man/sc99-paramString-method.Rd
man/sc99-qcprob-method.Rd
man/sc99-write.summary-method.Rd
tests
tests/checkFuncs
tests/sessionInfo.R
tests/sessionInfo.Rout.save
tests/testCobs.R
tests/testCobs.Rout.save
tests/testDesign.R
tests/testDesign.Rout.save
tests/testFit.R
tests/testFit.Rout.save
tests/testLoess.R
tests/testLoess.Rout.save
tests/testLogistic.R
tests/testLogistic.Rout.save
tests/testNormalize.R
tests/testRPPA.R
tests/testRPPA.Rout.save
tests/testRPPANormalizationParams.R
tests/testRPPANormalizationParams.Rout.save
tests/testRPPASet.R
tests/testRPPASet.Rout.save
tests/testRPPASpatialParams.R
tests/testRPPASpatialParams.Rout.save
tests/testRblock
vignettes
vignettes/SuperCurve.Rnw
SuperCurve documentation built on May 21, 2017, 3:46 a.m.