SuperCurve: RPPA Analysis Package

Analyze reverse phase protein lysate arrays.

AuthorKevin R. Coombes, Shannon Neeley, Corwin Joy, Jianhua Hu, Keith Baggerly, and P. Roebuck
Date of publication2015-08-02 23:18:50
Maintainer"P. Roebuck" <proebuck@mdanderson.org>
LicenseArtistic-2.0
Version1.5.15
http://r-forge.r-project.org/projects/supercurve/

View on R-Forge

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

actb Man page
actb.gray Man page
akt Man page
bar Man page
BoundedRange Man page
BoundedRange-class Man page
cas3 Man page
c.erk2 Man page
CobsFitClass-class Man page
coefficients,FitClass-method Man page
coefficients,LogisticFitClass-method Man page
coefficients,RPPAFit-method Man page
coef,FitClass-method Man page
coef,LogisticFitClass-method Man page
coef,RPPAFit-method Man page
coerce,character,Directory-method Man page
coerce,Directory,character-method Man page
ctnnb1 Man page
DefaultProgressMonitor Man page
DefaultProgressMonitor-class Man page
design40 Man page
dim,RPPADesign-method Man page
dim,RPPA-method Man page
Directory Man page
Directory-class Man page
DS5RPPAPreFitQC-class Man page
elapsed Man page
elapsed,ANY-method Man page
elapsed,DefaultProgressMonitor-method Man page
elapsed,ElapsedTime-method Man page
elapsed-method Man page
ElapsedTime Man page
ElapsedTime-class Man page
erk2 Man page
fak Man page
FitClass-class Man page
fitCurveAndSummarizeFromSettings Man page
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
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
getConfidenceInterval Man page
getRegisteredMethod Man page
getRegisteredMethodKeys Man page
getRegisteredModel Man page
getRegisteredModelKeys Man page
getRegisteredModelLabel Man page
getRegisteredNormalizationMethod Man page
getRegisteredNormalizationMethodKeys Man page
getRegisteredNormalizationMethodLabel Man page
getRegisteredObject Man page
getRegisteredObjectKeys Man page
getStages Man page
getSteps Man page
gsk3 Man page
hist,RPPAFit-method Man page
image,RPPADesign-method Man page
image,RPPAFit-method Man page
image,RPPA-method Man page
is.BoundedRange Man page
is.DefaultProgressMonitor Man page
is.Directory Man page
is.ElapsedTime Man page
is.FitClass Man page
is.ProgressMonitor Man page
is.RPPA Man page
is.RPPADesign Man page
is.RPPADesignParams Man page
is.RPPAFit Man page
is.RPPAFitParams Man page
is.RPPANormalizationParams Man page
is.RPPAPreFitQC Man page
is.RPPASet Man page
is.RPPASetSummary Man page
is.RPPASpatialParams Man page
is.SCProgressMonitor Man page
is.SuperCurveSettings Man page
jnk Man page
LoessFitClass-class Man page
LogisticFitClass-class Man page
names,RPPADesign-method Man page
normalize Man page
normalize,ANY-method Man page
normalize,MatrixLike-method Man page
normalize-method Man page
normalize,NULL-method Man page
normalize,RPPASet-method Man page
odc1 Man page
paramString Man page
paramString,ANY-method Man page
paramString-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
plot,RPPAFit,missing-method Man page
plot,RPPA,RPPADesign-method Man page
plugh Man page
progressDone Man page
progressDone<- Man page
progressDone<-,ANY,ANY-method Man page
progressDone,ANY-method Man page
progressDone<-,DefaultProgressMonitor,logical-method Man page
progressDone,DefaultProgressMonitor-method Man page
progressDone<--method Man page
progressDone-method Man page
progressDone<-,ProgressMonitor,ANY-method Man page
progressDone,ProgressMonitor-method Man page
progressError Man page
progressError<- Man page
progressError<-,ANY,ANY-method Man page
progressError,ANY-method Man page
progressError<-,DefaultProgressMonitor,logical-method Man page
progressError,DefaultProgressMonitor-method Man page
progressError<--method Man page
progressError-method Man page
progressError<-,ProgressMonitor,ANY-method Man page
progressError,ProgressMonitor-method Man page
progressLabel Man page
progressLabel<- Man page
progressLabel<-,ANY,ANY-method Man page
progressLabel,ANY-method Man page
progressLabel<-,DefaultProgressMonitor,character-method Man page
progressLabel,DefaultProgressMonitor-method Man page
progressLabel<--method Man page
progressLabel-method Man page
progressLabel<-,ProgressMonitor,ANY-method Man page
progressLabel,ProgressMonitor-method Man page
progressMarquee Man page
progressMarquee<- Man page
progressMarquee<-,ANY-method Man page
progressMarquee,ANY-method Man page
progressMarquee<--method Man page
progressMarquee-method Man page
progressMarquee<-,SCProgressMonitor,character-method Man page
progressMarquee,SCProgressMonitor-method Man page
progressMaximum Man page
progressMaximum<- Man page
progressMaximum<-,ANY,ANY-method Man page
progressMaximum,ANY-method Man page
progressMaximum,BoundedRange-method Man page
progressMaximum<-,BoundedRange,numeric-method Man page
progressMaximum,DefaultProgressMonitor-method Man page
progressMaximum<-,DefaultProgressMonitor,numeric-method Man page
progressMaximum<--method Man page
progressMaximum-method Man page
progressMaximum<-,ProgressMonitor,ANY-method Man page
progressMaximum,ProgressMonitor-method Man page
progressMinimum Man page
progressMinimum<- Man page
progressMinimum<-,ANY,ANY-method Man page
progressMinimum,ANY-method Man page
progressMinimum,BoundedRange-method Man page
progressMinimum<-,BoundedRange,numeric-method Man page
progressMinimum,DefaultProgressMonitor-method Man page
progressMinimum<-,DefaultProgressMonitor,numeric-method Man page
progressMinimum<--method Man page
progressMinimum-method Man page
progressMinimum<-,ProgressMonitor,ANY-method Man page
progressMinimum,ProgressMonitor-method Man page
ProgressMonitor-class Man page
progressStage Man page
progressStage<- Man page
progressStage<-,ANY-method Man page
progressStage,ANY-method Man page
progressStage<--method Man page
progressStage-method Man page
progressStage<-,SCProgressMonitor,character-method Man page
progressStage,SCProgressMonitor-method Man page
progressValue Man page
progressValue<- Man page
progressValue<-,ANY,ANY-method Man page
progressValue,ANY-method Man page
progressValue,BoundedRange-method Man page
progressValue<-,BoundedRange,numeric-method Man page
progressValue,DefaultProgressMonitor-method Man page
progressValue<-,DefaultProgressMonitor,numeric-method Man page
progressValue<--method Man page
progressValue-method Man page
progressValue<-,ProgressMonitor,ANY-method Man page
progressValue,ProgressMonitor-method Man page
qcprob Man page
qcprob,ANY-method Man page
qcprob,DS5RPPAPreFitQC-method Man page
qcprob-method Man page
qcprob,NULL-method Man page
qcprob,RPPAPreFitQC-method Man page
registerClassname Man page
registerMethod Man page
registerModel Man page
registerNormalizationMethod Man page
resid,RPPAFit-method Man page
residuals,RPPAFit-method Man page
RPPA Man page
rppaCell Man page
rppaCell-data Man page
RPPA-class Man page
RPPADesign Man page
RPPADesign-class Man page
RPPADesignFromParams Man page
RPPADesignParams Man page
RPPADesignParams-class Man page
RPPAFit Man page
RPPAFit-class Man page
RPPAFitFromParams Man page
RPPAFitParams Man page
RPPAFitParams-class Man page
RPPANormalizationParams Man page
RPPANormalizationParams-class Man page
RPPAPreFitQC Man page
RPPAPreFitQC-class Man page
RPPASet Man page
RPPASet-class Man page
RPPASetSummary Man page
RPPASetSummary-class Man page
rppaSingleSubgrid Man page
rppaSingleSubgrid-data Man page
RPPASpatialParams Man page
RPPASpatialParams-class Man page
rppaTriple Man page
rppaTriple-data Man page
rppaTumor Man page
rppaTumor-data Man page
SCProgressMonitor Man page
SCProgressMonitor-class Man page
sdesign Man page
seriesNames Man page
spatialAdjustment Man page
spatialAdjustmentFromParams Man page
spatialCorrection Man page
summary,DS5RPPAPreFitQC-method Man page
summary,RPPADesign-method Man page
summary,RPPAFit-method Man page
summary,RPPA-method Man page
summary,RPPAPreFitQC-method Man page
summary,RPPASet-method Man page
SuperCurve-package Man page
SuperCurveSettings Man page
SuperCurveSettings-class Man page
tDesign Man page
trimConc,CobsFitClass-method Man page
trimConc,FitClass-method Man page
trimConc,LoessFitClass-method Man page
trimConc,LogisticFitClass-method Man page
tripledesign Man page
waldo Man page
write.summary Man page
write.summary,ANY-method Man page
write.summary-method Man page
write.summary,RPPASet-method Man page
write.summary,RPPASetSummary-method Man page
write.summary,SuperCurveSettings-method Man page

Files

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

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