Learn R Programming

RPPASPACE (version 1.0.10)

Reverse-Phase Protein Array Super Position and Concentration Evaluation

Description

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. .

Copy Link

Version

Install

install.packages('RPPASPACE')

Monthly Downloads

141

Version

1.0.10

License

Artistic-2.0

Issues

4

Pull Requests

0

Stars

2

Forks

1

Maintainer

James M. Melott

Last Published

October 19th, 2023

Functions in RPPASPACE (1.0.10)

RPPAFit-class

Class “RPPAFit”
RPPAFitParams-class

Fitting Dilution Curves to Protein Lysate Arrays with Class “RPPAFitParams”
FitClass-class

Class “FitClass”
RPPASPACE-package

Reverse phase protein lysate array analysis
RPPAPreFitQC-class

Class “RPPAPreFitQC”
RPPA-class

Class “RPPA”
RPPASetSummary-class

Class “RPPASetSummary”
RPPASpatialParams-class

Class “RPPASpatialParams”
RPPANormalizationParams-class

Class “RPPANormalizationParams”
spatialCorrection

Spatial Correction
DS5RPPAPreFitQC-class

Class “DS5RPPAPreFitQC”
normalize

Normalization
getConfidenceInterval

Compute Confidence Intervals for a Model Fit to Dilution Series
paramString-method

Method “paramString”
registerNormalizationMethod

Normalization Method Registration Methods
registerModel

Model Registration Methods
normalize-method

Method “normalize”
RPPASPACESettings-class

Class “RPPASPACESettings”
write.summary-method

Method “write.summary”
qcprob-method

Method “qcprob”
registrationMethods

Generic Registration Methods
Directory-class

Class “Directory”
LoessFitClass-class

Class “LoessFitClass”
LogisticFitClass-class

Class “LogisticFitClass”
CobsFitClass-class

Class “CobsFitClass”
RPPADesignParams-class

Class “RPPADesignParams”
RPPASet-class

Class “RPPASet”