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:James M. Melott [aut, cre], Paul L. Roebuck [aut], Kevin R. Coombes [aut], Zhenlin Ju [aut], Huma Shehwana [aut], Shwetha V. Kumar [aut], E. Shannon Neeley [aut], Corwin Joy [aut], Jianhua Hu [aut], Keith A. Baggerly [aut], Rehan Akbani [aut], Mary A. Rohrdanz [ctb], Chris Wakefield [ctb], Doris R. Siwak [ctb], Yiling Lu [ctb], Bradley M. Broom [ctb], John N. Weinstein [ctb], Gordon B. Mills [ctb]

RPPASPACE_1.0.10.tar.gz
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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_1.0.10.tgz(r-4.3-emscripten)
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'))

Peer review:

Bug tracker:https://github.com/md-anderson-bioinformatics/rppaspace/issues

On CRAN:

23 exports 2 stars 1.02 score 38 dependencies 182 downloads

Last updated 8 months agofrom:6864c1f90518c7dd288fd565ee2128dfaaeb9fd3

Exports:fitCurveAndSummarizeFromSettingsgetRegisteredMethodgetRegisteredMethodKeysgetRegisteredModelgetRegisteredModelKeysgetRegisteredModelLabelgetRegisteredNormalizationMethodgetRegisteredNormalizationMethodKeysgetRegisteredNormalizationMethodLabelgetRegisteredObjectgetRegisteredObjectKeysnormalizeparamStringregisterClassnameregisterMethodregisterModelregisterNormalizationMethodRPPADesignParamsRPPAFitParamsRPPANormalizationParamsRPPASPACESettingsRPPASpatialParamswrite.summary

Dependencies:bmpclicobscodetoolscpp11DEoptimRdigestdoParalleldownloaderforeachglueigraphimageriteratorsjpeglatticelifecyclemagrittrMASSMatrixMatrixModelsmgcvnlmepkgconfigpngpurrrquantregRcppreadbitmaprlangrobustbaseSparseMstringistringrsurvivaltifftimeDatevctrs

Readme and manuals

Help Manual

Help pageTopics
Reverse phase protein lysate array analysisRPPASPACE-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 SeriesgetConfidenceInterval
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
Normalizationnormalize,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 MethodsgetRegisteredModel getRegisteredModelKeys getRegisteredModelLabel registerModel
Normalization Method Registration MethodsgetRegisteredNormalizationMethod 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 CorrectionspatialAdjustment spatialAdjustmentFromParams spatialCorrection
Method "write.summary"write.summary write.summary,ANY-method write.summary-method