Package: RPPASPACE 1.0.10
James M. Melott
RPPASPACE: Reverse-Phase Protein Array Super Position and Concentration Evaluation
Provides tools for the analysis of reverse-phase protein arrays (RPPAs), which are also known as 'tissue lysate arrays' or simply 'lysate arrays'. The package's primary purpose is to input a set of quantification files representing dilution series of samples and control points taken from scanned RPPA slides and determine a relative log concentration value for each valid dilution series present in each slide and provide graphical visualization of the input and output data and their relationships. Other optional features include generation of quality control scores for judging the quality of the input data, spatial adjustment of sample points based on controls added to the slides, and various types of normalization of calculated values across a set of slides. The package was derived from a previous package named SuperCurve. For a detailed description of data inputs and outputs, usage information, and a list of related papers describing methods used in the package please review the vignette 'Guide_to_RPPASPACE'. 'RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data'. Bioinformatics Nov 15;38(22):5131-5133. <doi:10.1093/bioinformatics/btac665>.
Authors:
RPPASPACE_1.0.10.tar.gz
RPPASPACE_1.0.10.zip(r-4.5)RPPASPACE_1.0.10.zip(r-4.4)RPPASPACE_1.0.10.zip(r-4.3)
RPPASPACE_1.0.10.tgz(r-4.4-any)RPPASPACE_1.0.10.tgz(r-4.3-any)
RPPASPACE_1.0.10.tar.gz(r-4.5-noble)RPPASPACE_1.0.10.tar.gz(r-4.4-noble)
RPPASPACE.pdf |RPPASPACE.html✨
RPPASPACE/json (API)
NEWS
| # Install 'RPPASPACE' in R: |
| install.packages('RPPASPACE', repos = c('https://md-anderson-bioinformatics.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/md-anderson-bioinformatics/rppaspace/issues
Last updated 1 months agofrom:b2d8972ec0
Exports:fitCurveAndSummarizeFromSettingsgetRegisteredMethodgetRegisteredMethodKeysgetRegisteredModelgetRegisteredModelKeysgetRegisteredModelLabelgetRegisteredNormalizationMethodgetRegisteredNormalizationMethodKeysgetRegisteredNormalizationMethodLabelgetRegisteredObjectgetRegisteredObjectKeysnormalizeparamStringregisterClassnameregisterMethodregisterModelregisterNormalizationMethodRPPADesignParamsRPPAFitParamsRPPANormalizationParamsRPPASPACESettingsRPPASpatialParamswrite.summary
Dependencies:bmpclicobscodetoolscpp11DEoptimRdigestdoParalleldownloaderforeachglueigraphimageriteratorsjpeglatticelifecyclemagrittrMASSMatrixMatrixModelsmgcvnlmepkgconfigpngpurrrquantregRcppreadbitmaprlangrobustbaseSparseMstringistringrsurvivaltifftimeDatevctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Reverse phase protein lysate array analysis | RPPASPACE-package |
| Class "CobsFitClass" | CobsFitClass-class fitSeries,CobsFitClass-method fitSlide,CobsFitClass-method fitted,CobsFitClass-method trimConc,CobsFitClass-method |
| Class "Directory" | coerce,character,Directory-method coerce,Directory,character-method Directory Directory-class is.Directory |
| Class "DS5RPPAPreFitQC" | DS5RPPAPreFitQC-class qcprob,DS5RPPAPreFitQC-method summary,DS5RPPAPreFitQC-method |
| Class "FitClass" | coef,FitClass-method coefficients,FitClass-method FitClass-class fitSeries,FitClass-method fitSlide,FitClass-method fitted,FitClass-method is.FitClass trimConc,FitClass-method |
| Compute Confidence Intervals for a Model Fit to Dilution Series | getConfidenceInterval |
| Class "LoessFitClass" | fitSeries,LoessFitClass-method fitSlide,LoessFitClass-method fitted,LoessFitClass-method LoessFitClass-class trimConc,LoessFitClass-method |
| Class "LogisticFitClass" | coef,LogisticFitClass-method coefficients,LogisticFitClass-method fitSeries,LogisticFitClass-method fitSlide,LogisticFitClass-method fitted,LogisticFitClass-method LogisticFitClass-class trimConc,LogisticFitClass-method |
| Normalization | normalize,MatrixLike-method |
| Method "normalize" | normalize normalize,ANY-method normalize,NULL-method normalize-method |
| Method "qcprob" | qcprob qcprob,ANY-method qcprob,NULL-method qcprob-method |
| Model Registration Methods | getRegisteredModel getRegisteredModelKeys getRegisteredModelLabel registerModel |
| Normalization Method Registration Methods | getRegisteredNormalizationMethod getRegisteredNormalizationMethodKeys getRegisteredNormalizationMethodLabel registerNormalizationMethod |
| Class "RPPA" | dim,RPPA-method image,RPPA-method is.RPPA plot,RPPA,ANY-method RPPA RPPA-class seriesNames seriesToUseToMakeCurve summary,RPPA-method |
| Class "RPPADesignParams" | is.RPPADesignParams paramString,RPPADesignParams-method plot,RPPA-method plot,RPPADesignParams-method RPPADesignParams RPPADesignParams-class |
| Class "RPPAFit" | coef,RPPAFit-method coefficients,RPPAFit-method fitted,RPPAFit-method hist,RPPAFit-method image,RPPAFit-method plot,RPPAFit,missing-method resid,RPPAFit-method residuals,RPPAFit-method RPPAFit-class summary,RPPAFit-method |
| Fitting Dilution Curves to Protein Lysate Arrays with Class "RPPAFitParams" | is.RPPAFit is.RPPAFitParams paramString,RPPAFitParams-method RPPAFit RPPAFitFromParams RPPAFitParams RPPAFitParams-class |
| Class "RPPANormalizationParams" | is.RPPANormalizationParams paramString,RPPANormalizationParams-method RPPANormalizationParams RPPANormalizationParams-class |
| Class "RPPAPreFitQC" | is.RPPAPreFitQC qcprob,RPPAPreFitQC-method RPPAPreFitQC RPPAPreFitQC-class summary,RPPAPreFitQC-method |
| Class "RPPASet" | is.RPPASet normalize,RPPASet-method RPPASet RPPASet-class summary,RPPASet-method write.summary,RPPASet-method |
| Class "RPPASetSummary" | is.RPPASetSummary RPPASetSummary RPPASetSummary-class write.summary,RPPASetSummary-method |
| Class "RPPASPACESettings" | fitCurveAndSummarizeFromSettings is.RPPASPACESettings paramString,RPPASPACESettings-method RPPASPACESettings RPPASPACESettings-class write.summary,RPPASPACESettings-method |
| Class "RPPASpatialParams" | is.RPPASpatialParams paramString,RPPASpatialParams-method RPPASpatialParams RPPASpatialParams-class |
| Spatial Correction | spatialAdjustment spatialAdjustmentFromParams spatialCorrection |
| Method "write.summary" | write.summary write.summary,ANY-method write.summary-method |
