RPPA Analysis Package


[Up] [Top]

Documentation for package ‘SuperCurve’ version 1.5.15

Help Pages

A B C D E F G H I J L N O P Q R S T W

SuperCurve-package Reverse phase protein lysate array analysis

-- A --

actb ACTB, CAS3, FAK, and ODC1 expression in 14 fed/starved cell lines
actb.gray ACTB, CAS3, FAK, and ODC1 expression in 14 fed/starved cell lines
akt AKT, ERK2, and CTNNB1 expression in cell lines

-- B --

bar FOO, BAR, PLUGH, and WALDO expression
BoundedRange Class "BoundedRange"
BoundedRange-class Class "BoundedRange"

-- C --

c.erk2 AKT, ERK2, and CTNNB1 expression in cell lines
cas3 ACTB, CAS3, FAK, and ODC1 expression in 14 fed/starved cell lines
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"
ctnnb1 AKT, ERK2, and CTNNB1 expression in cell lines

-- D --

DefaultProgressMonitor Class "DefaultProgressMonitor"
DefaultProgressMonitor-class Class "DefaultProgressMonitor"
design40 AKT, ERK2, and CTNNB1 expression in cell lines
dim-method Class "RPPA"
dim-method Class "RPPADesign" and Class "RPPADesignParams"
Directory Class "Directory"
Directory-class Class "Directory"
DS5RPPAPreFitQC-class Class "DS5RPPAPreFitQC"

-- E --

elapsed Method "elapsed"
elapsed-method Class "DefaultProgressMonitor"
elapsed-method Class "ElapsedTime"
elapsed-method Method "elapsed"
ElapsedTime Class "ElapsedTime"
ElapsedTime-class Class "ElapsedTime"
erk2 ERK2, GSK3, and JNK expression in tumor samples

-- F --

fak ACTB, CAS3, FAK, and ODC1 expression in 14 fed/starved cell lines
FitClass-class Class "FitClass"
fitCurveAndSummarizeFromSettings Class "SuperCurveSettings"
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"
foo FOO, BAR, PLUGH, and WALDO expression

-- 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
getStages Class "SCProgressMonitor"
getSteps Class "RPPADesign" and Class "RPPADesignParams"
gsk3 ERK2, GSK3, and JNK expression in tumor samples

-- H --

hist-method Class "RPPAFit"

-- I --

image-method Class "RPPA"
image-method Class "RPPADesign" and Class "RPPADesignParams"
image-method Class "RPPAFit"
is.BoundedRange Class "BoundedRange"
is.DefaultProgressMonitor Class "DefaultProgressMonitor"
is.Directory Class "Directory"
is.ElapsedTime Class "ElapsedTime"
is.FitClass Class "FitClass"
is.ProgressMonitor Class "ProgressMonitor"
is.RPPA Class "RPPA"
is.RPPADesign Class "RPPADesign" and Class "RPPADesignParams"
is.RPPADesignParams Class "RPPADesign" and 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.RPPASpatialParams Class "RPPASpatialParams"
is.SCProgressMonitor Class "SCProgressMonitor"
is.SuperCurveSettings Class "SuperCurveSettings"

-- J --

jnk ERK2, GSK3, and JNK expression in tumor samples

-- L --

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

-- N --

names-method Class "RPPADesign" and Class "RPPADesignParams"
normalize Method "normalize"
normalize-method Class "RPPASet"
normalize-method Normalization
normalize-method Method "normalize"

-- O --

odc1 ACTB, CAS3, FAK, and ODC1 expression in 14 fed/starved cell lines

-- P --

paramString-method Class "RPPADesign" and 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 "SuperCurveSettings"
plot-method Class "RPPADesign" and Class "RPPADesignParams"
plot-method Class "RPPAFit"
plugh FOO, BAR, PLUGH, and WALDO expression
progressDone Methods for Manipulating Progress Monitors
progressDone-method Class "DefaultProgressMonitor"
progressDone-method Class "ProgressMonitor"
progressDone-method Methods for Manipulating Progress Monitors
progressDone<- Methods for Manipulating Progress Monitors
progressDone<--method Class "DefaultProgressMonitor"
progressDone<--method Class "ProgressMonitor"
progressDone<--method Methods for Manipulating Progress Monitors
progressError Methods for Manipulating Progress Monitors
progressError-method Class "DefaultProgressMonitor"
progressError-method Class "ProgressMonitor"
progressError-method Methods for Manipulating Progress Monitors
progressError<- Methods for Manipulating Progress Monitors
progressError<--method Class "DefaultProgressMonitor"
progressError<--method Class "ProgressMonitor"
progressError<--method Methods for Manipulating Progress Monitors
progressLabel Methods for Manipulating Progress Monitors
progressLabel-method Class "DefaultProgressMonitor"
progressLabel-method Class "ProgressMonitor"
progressLabel-method Methods for Manipulating Progress Monitors
progressLabel<- Methods for Manipulating Progress Monitors
progressLabel<--method Class "DefaultProgressMonitor"
progressLabel<--method Class "ProgressMonitor"
progressLabel<--method Methods for Manipulating Progress Monitors
progressMarquee Methods for Manipulating SuperCurve Progress Models
progressMarquee-method Class "SCProgressMonitor"
progressMarquee-method Methods for Manipulating SuperCurve Progress Models
progressMarquee<- Methods for Manipulating SuperCurve Progress Models
progressMarquee<--method Class "SCProgressMonitor"
progressMarquee<--method Methods for Manipulating SuperCurve Progress Models
progressMaximum Methods for Manipulating Progress Monitors
progressMaximum-method Class "BoundedRange"
progressMaximum-method Class "DefaultProgressMonitor"
progressMaximum-method Class "ProgressMonitor"
progressMaximum-method Methods for Manipulating Progress Monitors
progressMaximum<- Methods for Manipulating Progress Monitors
progressMaximum<--method Class "BoundedRange"
progressMaximum<--method Class "DefaultProgressMonitor"
progressMaximum<--method Class "ProgressMonitor"
progressMaximum<--method Methods for Manipulating Progress Monitors
progressMinimum Methods for Manipulating Progress Monitors
progressMinimum-method Class "BoundedRange"
progressMinimum-method Class "DefaultProgressMonitor"
progressMinimum-method Class "ProgressMonitor"
progressMinimum-method Methods for Manipulating Progress Monitors
progressMinimum<- Methods for Manipulating Progress Monitors
progressMinimum<--method Class "BoundedRange"
progressMinimum<--method Class "DefaultProgressMonitor"
progressMinimum<--method Class "ProgressMonitor"
progressMinimum<--method Methods for Manipulating Progress Monitors
ProgressMonitor-class Class "ProgressMonitor"
progressStage Methods for Manipulating SuperCurve Progress Models
progressStage-method Class "SCProgressMonitor"
progressStage-method Methods for Manipulating SuperCurve Progress Models
progressStage<- Methods for Manipulating SuperCurve Progress Models
progressStage<--method Class "SCProgressMonitor"
progressStage<--method Methods for Manipulating SuperCurve Progress Models
progressValue Methods for Manipulating Progress Monitors
progressValue-method Class "BoundedRange"
progressValue-method Class "DefaultProgressMonitor"
progressValue-method Class "ProgressMonitor"
progressValue-method Methods for Manipulating Progress Monitors
progressValue<- Methods for Manipulating Progress Monitors
progressValue<--method Class "BoundedRange"
progressValue<--method Class "DefaultProgressMonitor"
progressValue<--method Class "ProgressMonitor"
progressValue<--method Methods for Manipulating Progress Monitors

-- 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"
rppaCell AKT, ERK2, and CTNNB1 expression in cell lines
rppaCell-data AKT, ERK2, and CTNNB1 expression in cell lines
RPPADesign Class "RPPADesign" and Class "RPPADesignParams"
RPPADesign-class Class "RPPADesign" and Class "RPPADesignParams"
RPPADesignFromParams Class "RPPADesign" and Class "RPPADesignParams"
RPPADesignParams Class "RPPADesign" and Class "RPPADesignParams"
RPPADesignParams-class Class "RPPADesign" and 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"
rppaSingleSubgrid FOO, BAR, PLUGH, and WALDO expression
rppaSingleSubgrid-data FOO, BAR, PLUGH, and WALDO expression
RPPASpatialParams Class "RPPASpatialParams"
RPPASpatialParams-class Class "RPPASpatialParams"
rppaTriple ACTB, CAS3, FAK, and ODC1 expression in 14 fed/starved cell lines
rppaTriple-data ACTB, CAS3, FAK, and ODC1 expression in 14 fed/starved cell lines
rppaTumor ERK2, GSK3, and JNK expression in tumor samples
rppaTumor-data ERK2, GSK3, and JNK expression in tumor samples

-- S --

SCProgressMonitor Class "SCProgressMonitor"
SCProgressMonitor-class Class "SCProgressMonitor"
sdesign FOO, BAR, PLUGH, and WALDO expression
seriesNames Class "RPPADesign" and Class "RPPADesignParams"
spatialAdjustment Spatial Correction
spatialAdjustmentFromParams Spatial Correction
spatialCorrection Spatial Correction
summary-method Class "RPPA"
summary-method Class "RPPADesign" and Class "RPPADesignParams"
summary-method Class "RPPAFit"
summary-method Class "RPPASet"
summary-method Class "RPPAPreFitQC"
summary-method Class "DS5RPPAPreFitQC"
SuperCurveSettings Class "SuperCurveSettings"
SuperCurveSettings-class Class "SuperCurveSettings"

-- T --

tDesign ERK2, GSK3, and JNK expression in tumor samples
trimConc-method Class "FitClass"
trimConc-method Class "LogisticFitClass"
trimConc-method Class "CobsFitClass"
trimConc-method Class "LoessFitClass"
tripledesign ACTB, CAS3, FAK, and ODC1 expression in 14 fed/starved cell lines

-- W --

waldo FOO, BAR, PLUGH, and WALDO expression
write.summary Method "write.summary"
write.summary-method Class "RPPASet"
write.summary-method Class "RPPASetSummary"
write.summary-method Class "SuperCurveSettings"
write.summary-method Method "write.summary"