# Thermal proximity co-aggregation with R

## Documentation for package ‘Rtpca’ version 1.4.0

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

## Help Pages

CommonFeatures | Extract CommonFeatures
CommonFeatures-method | Extract CommonFeatures
ComplexAnnotation | Extract ComplexAnnotation
ComplexAnnotation-method | Extract ComplexAnnotation
ComplexBackgroundDistributionList | Extract ComplexBackgroundDistributionList
ComplexBackgroundDistributionList-method | Extract ComplexBackgroundDistributionList
ComplexRocTable | Extract ComplexRocTable
ComplexRocTable-method | Extract ComplexRocTable
ContrastCondName | Extract ContrastCondName
ContrastCondName-method | Extract ContrastCondName
ContrastDistMat | Extract ContrastDistMat
ContrastDistMat-method | Extract ContrastDistMat
ContrastList | Extract ContrastList
ContrastList-method | Extract ContrastList
createDistMat | Create distance matrix of all vs all protein melting profiles
CtrlCondName | Extract CtrlCondName
CtrlCondName-method | Extract CtrlCondName
diffTpcaResultTable | Extract diffTpcaResultTable
diffTpcaResultTable-method | Extract diffTpcaResultTable
DistMat | Extract DistMat
DistMat-method | Extract DistMat
DistMethod | Extract DistMethod
DistMethod-method | Extract DistMethod
ObjList | Extract ObjList
ObjList-method | Extract ObjList
ori_et_al_complexes_df | Data frame of annotated protein complexes by Ori et al.
ori_et_al_complex_ppis | Data frame of eukaryotic protein-protein interactions inferred from annotated protein complexes by Ori et al. and StringDB interations with a combined score of at least 900
plotComplexRoc | Plot Complex ROC curve
plotDiffTpcaVolcano | Plot differential TPCA analysis results
plotPPiProfiles | Plot thermal profile of protein pairs
plotPPiRoc | Plot PPI ROC curve
plotTpcaVolcano | Plot TPCA analysis results
PPiAnnotation | Extract PPiAnnotation
PPiAnnotation-method | Extract PPiAnnotation
PPiRocTable | Extract PPiRocTable
PPiRocTable-method | Extract PPiRocTable
PPiRocTableAnno | Extract PPiRocTableAnno
PPiRocTableAnno-method | Extract PPiRocTableAnno
runDiffTPCA | Run differential TPCA analysis
runTPCA | Run the TPCA analysis
SetCommonFeatures | Set CommonFeatures
SetCommonFeatures-method | Set CommonFeatures
SetComplexAnnotation | Set ComplexAnnotation
SetComplexAnnotation-method | Set ComplexAnnotation
SetComplexBackgroundDistributionList | Set ComplexBackgroundDistributionList
SetComplexBackgroundDistributionList-method | Set ComplexBackgroundDistributionList
SetComplexRocTable | Set ComplexRocTable
SetComplexRocTable-method | Set ComplexRocTable
SetContrastCondName | Set ContrastCondName
SetContrastCondName-method | Set ContrastCondName
SetContrastDistMat | Set ContrastDistMat
SetContrastDistMat-method | Set ContrastDistMat
SetCtrlCondName | Set CtrlCondName
SetCtrlCondName-method | Set CtrlCondName
SetDiffTpcaResultTable | Set diffTpcaResultTable
SetDiffTpcaResultTable-method | Set diffTpcaResultTable
SetDistMat | Set DistMat
SetDistMat-method | Set DistMat
SetDistMethod | Set distMethod
SetDistMethod-method | Set distMethod
SetPPiRocTable | Set PPiRocTable
SetPPiRocTable-method | Set PPiRocTable
SetPPiRocTableAnno | Set PPiRocTableAnno
SetPPiRocTableAnno-method | Set PPiRocTableAnno
SetSummaryMethod | Set summaryMethod
SetSummaryMethod-method | Set summaryMethod
SetTpcaResultTable | Set TpcaResultTable
SetTpcaResultTable-method | Set TpcaResultTable
string_ppi_df | Data frame of annotated human protein-protein interactions retrieved from stringDB with a combined interaction score equal or higher than 700
SummaryMethod | Extract SummaryMethod
SummaryMethod-method | Extract SummaryMethod
tpcaResult | S4 TPCA Result Class
tpcaResult-class | S4 TPCA Result Class
tpcaResultTable | Extract tpcaResultTable
tpcaResultTable-method | Extract tpcaResultTable