addData |
Import additional CEL files into a DataTreeSet |
addData,DataTreeSet-method |
Class DataTreeSet |
addData-methods |
Import additional CEL files into a DataTreeSet |
AnalysisTreeSet |
Class AnalysisTreeSet |
AnalysisTreeSet-class |
Class AnalysisTreeSet |
arrayInfo |
Class ProjectInfo |
arrayInfo,ProjectInfo-method |
Class ProjectInfo |
arrayInfo<- |
Class ProjectInfo |
arrayInfo<-,ProjectInfo,character-method |
Class ProjectInfo |
attachBgrd |
Attach/Remove Background Intensities |
attachBgrd,DataTreeSet-method |
Class DataTreeSet |
attachBgrd-methods |
Attach/Remove Background Intensities |
attachCall |
Attach/Remove Detecion Call Measures |
attachCall,CallTreeSet-method |
Class CallTreeSet |
attachCall-methods |
Attach/Remove Detecion Call Measures |
attachExpr |
Attach/Remove Expression Measures |
attachExpr,ExprTreeSet-method |
Class ExprTreeSet |
attachExpr-methods |
Attach/Remove Expression Measures |
attachInten |
Attach/Remove Intensities |
attachInten,DataTreeSet-method |
Class DataTreeSet |
attachInten-methods |
Attach/Remove Intensities |
attachMask |
Attach/Remove Scheme Mask |
attachMask,DataTreeSet-method |
Class DataTreeSet |
attachMask,SchemeTreeSet-method |
Class SchemeTreeSet |
attachMask-methods |
Attach/Remove Scheme Mask |
attachPVal |
Attach/Remove Detecion Call Measures |
attachPVal,CallTreeSet-method |
Class CallTreeSet |
attachPVal-methods |
Attach/Remove Detecion Call Measures |
authorInfo |
Class ProjectInfo |
authorInfo,ProjectInfo-method |
Class ProjectInfo |
authorInfo<- |
Class ProjectInfo |
authorInfo<-,ProjectInfo,character-method |
Class ProjectInfo |
callFilter |
Detection Call Filter |
callFilter,PreFilter-method |
Class PreFilter |
callFilter,UniFilter-method |
Class UniFilter |
callFilter-methods |
Detection Call Filter |
callFilter<- |
Detection Call Filter |
callFilter<-,PreFilter,character-method |
Class PreFilter |
callFilter<-,UniFilter,character-method |
Class UniFilter |
callplot |
Barplot of Percent Present and Absent Calls. |
callplot,CallTreeSet-method |
Class CallTreeSet |
callplot-methods |
Barplot of Percent Present and Absent Calls. |
CallTreeSet |
Class CallTreeSet |
callTreeset |
Class FilterTreeSet |
callTreeset,FilterTreeSet-method |
Class FilterTreeSet |
CallTreeSet-class |
Class CallTreeSet |
cellineInfo |
Class ProjectInfo |
cellineInfo,ProjectInfo-method |
Class ProjectInfo |
cellineInfo<- |
Class ProjectInfo |
cellineInfo<-,ProjectInfo,character-method |
Class ProjectInfo |
chipMask |
Class SchemeTreeSet |
chipMask,SchemeTreeSet-method |
Class SchemeTreeSet |
chipMask<- |
Class SchemeTreeSet |
chipMask<-,SchemeTreeSet,data.frame-method |
Class SchemeTreeSet |
chipName |
Class SchemeTreeSet |
chipName,ProcesSet-method |
Class ProcesSet |
chipName,SchemeTreeSet-method |
Class SchemeTreeSet |
chipType |
Class SchemeTreeSet |
chipType,ProcesSet-method |
Class ProcesSet |
chipType,SchemeTreeSet-method |
Class SchemeTreeSet |
chipType<- |
Class SchemeTreeSet |
chipType<-,SchemeTreeSet,character-method |
Class SchemeTreeSet |
cvFilter |
Coefficient of Variation Filter |
cvFilter,PreFilter-method |
Class PreFilter |
cvFilter-methods |
Coefficient of Variation Filter |
cvFilter<- |
Coefficient of Variation Filter |
cvFilter<-,PreFilter,numeric-method |
Class PreFilter |
existsROOTFile |
Test for Existing ROOT File |
exonLevel |
Conversion of Parameter exonlevel to Integer |
export |
Export data as text files |
export,ProcesSet-method |
Class ProcesSet |
export,SchemeTreeSet-method |
Class SchemeTreeSet |
export,TreeSet-method |
Class TreeSet |
export-methods |
Export data as text files |
export.call |
Export data as text files |
export.data |
Export data as text files |
export.expr |
Export data as text files |
export.filter |
Export filter data as text files |
export.root |
Export data from ROOT file |
export.scheme |
Export data as text files |
express |
Compute expression levels from raw data |
exprs |
Get/Set Expression Values |
exprs,ExprTreeSet-method |
Class ExprTreeSet |
exprs-methods |
Get/Set Expression Values |
exprs<- |
Get/Set Expression Values |
exprs<-,ExprTreeSet,data.frame-method |
Class ExprTreeSet |
ExprTreeSet |
Class ExprTreeSet |
exprTreeset |
Class FilterTreeSet |
exprTreeset,FilterTreeSet-method |
Class FilterTreeSet |
ExprTreeSet-class |
Class ExprTreeSet |
exprType |
Class ExprTreeSet |
exprType,ExprTreeSet-method |
Class ExprTreeSet |
exprType<- |
Class ExprTreeSet |
exprType<-,ExprTreeSet,character-method |
Class ExprTreeSet |
extenPart |
Get Extension of Tree Names |
image |
Display an Image |
image,DataTreeSet-method |
Class DataTreeSet |
image-methods |
Display an Image |
image.dev |
Image for Device |
import.data |
Import CEL files into a DataTreeSet |
import.exon.scheme |
Import CLF, PGF and annotation files into a SchemeTreeSet |
import.expr.scheme |
Import CDF, probe and annotation files into a SchemeTreeSet |
import.genome.scheme |
Import CLF, PGF and annotation files into a SchemeTreeSet |
ini.call |
Informative/Non-Informative Call |
initialize |
Initialize Classes |
initialize,AnalysisTreeSet-method |
Initialize Classes |
initialize,CallTreeSet-method |
Initialize Classes |
initialize,DataTreeSet-method |
Initialize Classes |
initialize,ExprTreeSet-method |
Initialize Classes |
initialize,Filter-method |
Initialize Classes |
initialize,FilterTreeSet-method |
Initialize Classes |
initialize,PreFilter-method |
Initialize Classes |
initialize,ProcesSet-method |
Initialize Classes |
initialize,ProjectInfo-method |
Initialize Classes |
initialize,SchemeTreeSet-method |
Initialize Classes |
initialize,TreeSet-method |
Initialize Classes |
initialize,UniFilter-method |
Initialize Classes |
initialize-methods |
Initialize Classes |
intensity |
Get/Set Data Values |
intensity,DataTreeSet-method |
Class DataTreeSet |
intensity-methods |
Get/Set Data Values |
intensity<- |
Get/Set Data Values |
intensity<-,DataTreeSet,data.frame-method |
Class DataTreeSet |
isROOTFile |
Test for ROOT File |
pm |
Methods for accessing perfect matches and mismatches |
pm,DataTreeSet-method |
Class DataTreeSet |
pm-methods |
Methods for accessing perfect matches and mismatches |
pmplot |
Barplot of PM and MM Intensities. |
pmplot,DataTreeSet-method |
Class DataTreeSet |
pmplot-methods |
Barplot of PM and MM Intensities. |
PreFilter |
Constructor for Class PreFilter |
prefilter |
Function for Applying a PreFilter to an ExprTreeSet |
PreFilter-class |
Class PreFilter |
presCall |
Get/Set Present Call Values |
presCall,CallTreeSet-method |
Class CallTreeSet |
presCall-methods |
Get/Set Present Call Values |
presCall<- |
Get/Set Present Call Values |
presCall<-,CallTreeSet,data.frame-method |
Class CallTreeSet |
primcellInfo |
Class ProjectInfo |
primcellInfo,ProjectInfo-method |
Class ProjectInfo |
primcellInfo<- |
Class ProjectInfo |
primcellInfo<-,ProjectInfo,character-method |
Class ProjectInfo |
probeInfo |
Class SchemeTreeSet |
probeInfo,SchemeTreeSet-method |
Class SchemeTreeSet |
ProcesSet |
Class ProcesSet |
ProcesSet-class |
Class ProcesSet |
ProjectInfo |
Constructor for Class ProjectInfo |
projectInfo |
Class ProjectInfo |
projectInfo,DataTreeSet-method |
Class DataTreeSet |
projectInfo,ProjectInfo-method |
Class ProjectInfo |
ProjectInfo-class |
Class ProjectInfo |
projectInfo<- |
Class ProjectInfo |
projectInfo<-,DataTreeSet,ProjectInfo-method |
Class DataTreeSet |
projectInfo<-,ProjectInfo,character-method |
Class ProjectInfo |
pvalData |
Get/Set Present Call Values |
pvalData,CallTreeSet-method |
Class CallTreeSet |
pvalData-methods |
Get/Set Present Call Values |
pvalData<- |
Get/Set Present Call Values |
pvalData<-,CallTreeSet,data.frame-method |
Class CallTreeSet |
ratioFilter |
Ratio Filter |
ratioFilter,PreFilter-method |
Class PreFilter |
ratioFilter-methods |
Ratio Filter |
ratioFilter<- |
Ratio Filter |
ratioFilter<-,PreFilter,numeric-method |
Class PreFilter |
rawCELName |
Method for getting names of the raw CEL-files |
rawCELName,DataTreeSet-method |
Class DataTreeSet |
rawCELName-methods |
Method for getting names of the raw CEL-files |
removeBgrd |
Attach/Remove Background Intensities |
removeBgrd,DataTreeSet-method |
Class DataTreeSet |
removeBgrd-methods |
Attach/Remove Background Intensities |
removeCall |
Attach/Remove Detecion Call Measures |
removeCall,CallTreeSet-method |
Class CallTreeSet |
removeCall-methods |
Attach/Remove Detecion Call Measures |
removeExpr |
Attach/Remove Expression Measures |
removeExpr,ExprTreeSet-method |
Class ExprTreeSet |
removeExpr-methods |
Attach/Remove Expression Measures |
removeInten |
Attach/Remove Intensities |
removeInten,DataTreeSet-method |
Class DataTreeSet |
removeInten-methods |
Attach/Remove Intensities |
removeMask |
Attach/Remove Scheme Mask |
removeMask,DataTreeSet-method |
Class DataTreeSet |
removeMask,SchemeTreeSet-method |
Class SchemeTreeSet |
removeMask-methods |
Attach/Remove Scheme Mask |
removePVal |
Attach/Remove Detecion Call Measures |
removePVal,CallTreeSet-method |
Class CallTreeSet |
removePVal-methods |
Attach/Remove Detecion Call Measures |
rma |
Robust Multi-Array Average Expression Measure |
ROOT |
ROOT An Object-Oriented Data Analysis Framework |
root.browser |
Open the ROOT object browser |
root.browser,TreeSet-method |
Class TreeSet |
root.call |
Create class CallTreeSet accessing ROOT detection call file |
root.data |
Create class DataTreeSet accessing ROOT data file |
root.density |
ROOT Density Plot |
root.expr |
Create class ExprTreeSet accessing ROOT expression file |
root.graph1D |
ROOT 1D-Graph |
root.graph2D |
ROOT 2D-Graph |
root.hist1D |
ROOT 1D-Histogram |
root.hist2D |
ROOT 2D-Histogram |
root.hist3D |
ROOT 3D-Histogram |
root.image |
ROOT Image |
root.merge.data |
Create class DataTreeSet by merging ROOT data files |
root.mvaplot |
ROOT M vs A Plot |
root.profile |
ROOT Profile Plot |
root.scheme |
Create class SchemeTreeSet accessing ROOT scheme file |
rootFile |
Class TreeSet |
rootFile,TreeSet-method |
Class TreeSet |
rootFile<- |
Class TreeSet |
rootFile<-,TreeSet,character-method |
Class TreeSet |
sampleInfo |
Class ProjectInfo |
sampleInfo,ProjectInfo-method |
Class ProjectInfo |
sampleInfo<- |
Class ProjectInfo |
sampleInfo<-,ProjectInfo,character-method |
Class ProjectInfo |
schemeFile |
Class ProcesSet |
schemeFile,ProcesSet-method |
Class ProcesSet |
schemeFile<- |
Class ProcesSet |
schemeFile<-,ProcesSet,character-method |
Class ProcesSet |
schemeSet |
Class ProcesSet |
schemeSet,ProcesSet-method |
Class ProcesSet |
schemeSet<- |
Class ProcesSet |
schemeSet<-,ProcesSet,SchemeTreeSet-method |
Class ProcesSet |
SchemeTreeSet |
Class SchemeTreeSet |
SchemeTreeSet-class |
Class SchemeTreeSet |
se.exprs |
Class ExprTreeSet |
se.exprs,ExprTreeSet-method |
Class ExprTreeSet |
setName |
Class TreeSet |
setName,TreeSet-method |
Class TreeSet |
setName<- |
Class TreeSet |
setName<-,TreeSet,character-method |
Class TreeSet |
setType |
Class TreeSet |
setType,TreeSet-method |
Class TreeSet |
setType<- |
Class TreeSet |
setType<-,TreeSet,character-method |
Class TreeSet |
show,ProjectInfo-method |
Class ProjectInfo |
sourceInfo |
Class ProjectInfo |
sourceInfo,ProjectInfo-method |
Class ProjectInfo |
sourceInfo<- |
Class ProjectInfo |
sourceInfo<-,ProjectInfo,character-method |
Class ProjectInfo |
summarize |
Probe Set Summarizing Functions |
summarize.mas4 |
Probe Set Summarizing Functions |
summarize.mas5 |
Probe Set Summarizing Functions |
summarize.rma |
Probe Set Summarizing Functions |
validBgrd |
Class DataTreeSet |
validBgrd,DataTreeSet-method |
Class DataTreeSet |
validCall |
Get Valid Detection Call Values |
validCall,CallTreeSet-method |
Class CallTreeSet |
validData |
Extract Subset of Data |
validData,AnalysisTreeSet-method |
Class AnalysisTreeSet |
validData,DataTreeSet-method |
Class DataTreeSet |
validData,FilterTreeSet-method |
Class FilterTreeSet |
validData,ProcesSet-method |
Class ProcesSet |
validExpr |
Get Valid Expression Levels |
validExpr,ExprTreeSet-method |
Class ExprTreeSet |
validFilter |
Class AnalysisTreeSet |
validFilter,AnalysisTreeSet-method |
Class AnalysisTreeSet |
validPVal |
Get Valid Detection Call Values |
validPVal,CallTreeSet-method |
Class CallTreeSet |
validTreetype |
Validate Tree Type |
varFilter |
Variance Filter |
varFilter,PreFilter-method |
Class PreFilter |
varFilter-methods |
Variance Filter |
varFilter<- |
Variance Filter |
varFilter<-,PreFilter,numeric-method |
Class PreFilter |
volcanoplot |
Volcano Plot |
volcanoplot,AnalysisTreeSet-method |
Class AnalysisTreeSet |
volcanoplot-methods |
Volcano Plot |
xps |
xps Package Overview |
xpsBgCorrect |
Background Correction |
xpsBgCorrect,DataTreeSet-method |
Class DataTreeSet |
xpsBgCorrect-methods |
Background Correction |
xpsDABGCall |
Detection Above Background Call |
xpsDABGCall,DataTreeSet-method |
Class DataTreeSet |
xpsDABGCall-methods |
Detection Above Background Call |
xpsINICall |
Informative/Non-Informative Call |
xpsINICall,DataTreeSet-method |
Class DataTreeSet |
xpsINICall-methods |
Informative/Non-Informative Call |
xpsMAS4 |
MAS 4.0 Expression Measure |
xpsMAS4,DataTreeSet-method |
Class DataTreeSet |
xpsMAS4-methods |
MAS 4.0 Expression Measure |
xpsMAS5 |
MAS 5.0 Expression Measure |
xpsMAS5,DataTreeSet-method |
Class DataTreeSet |
xpsMAS5-methods |
MAS 5.0 Expression Measure |
xpsMAS5Call |
MAS 5.0 Absolute Detection Call |
xpsMAS5Call,DataTreeSet-method |
Class DataTreeSet |
xpsMAS5Call-methods |
MAS 5.0 Absolute Detection Call |
xpsNormalize |
Normalization on Affymetrix Probe Level Data or on Expression Levels |
xpsNormalize,DataTreeSet-method |
Class DataTreeSet |
xpsNormalize,ExprTreeSet-method |
Class ExprTreeSet |
xpsNormalize-methods |
Normalization on Affymetrix Probe Level Data or on Expression Levels |
xpsOptions |
xps Options |
xpsPreFilter |
Function for Applying a PreFilter to an ExprTreeSet |
xpsPreFilter,ExprTreeSet-method |
Class ExprTreeSet |
xpsPreFilter-methods |
Function for Applying a PreFilter to an ExprTreeSet |
xpsPreprocess |
Compute expression levels from raw data |
xpsPreprocess,DataTreeSet-method |
Class DataTreeSet |
xpsPreprocess-methods |
Compute expression levels from raw data |
xpsRMA |
Robust Multi-Array Average Expression Measure |
xpsRMA,DataTreeSet-method |
Class DataTreeSet |
xpsRMA-methods |
Robust Multi-Array Average Expression Measure |
xpsSummarize |
Probe Set Summarizing Functions |
xpsSummarize,DataTreeSet-method |
Class DataTreeSet |
xpsSummarize-methods |
Probe Set Summarizing Functions |
xpsUniFilter |
Function for Applying an UniFilter to an ExprTreeSet |
xpsUniFilter,ExprTreeSet-method |
Class ExprTreeSet |
xpsUniFilter-methods |
Function for Applying an UniFilter to an ExprTreeSet |