RPPanalyzer: Reads, Annotates, and Normalizes Reverse Phase Protein Array Data
Version 1.4.3

Reads in sample description and slide description files and annotates the expression values taken from GenePix results files (text file format used by many microarray scanner and software providers). After normalization data can be visualized as boxplot, heatmap or dotplot.

Browse man pages Browse package API and functions Browse package files

AuthorHeiko Mannsperger with contributions of Stephan Gade
Date of publication2016-02-11 16:43:06
MaintainerAstrid Wachter <astrid.wachter@med.uni-goettingen.de>
LicenseLGPL
Version1.4.3
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("RPPanalyzer")

Man pages

averageData: Average biological replicates over different slides.
calcLinear: Calculates sample concentrations using linear model fit
calcLogistic: Calculates sample concentrations using sigmoid model fit
calcSdc: Calculates the concentration of serial diluted samples
correctBG: Corrects for background in an RPPA data set
correctDilinterc: Dilution series intersect correction
curvePredictSigmoid: Sigmoidal curve prediction.
dataI: Reverse phase protein array rawdata, samples serially diluted
dataII: Reverse phase protein array data, samples from a stimulation...
dataIII: Reverse phase protein array data from original cancer...
dataPreproc: Data preprocessing
getErrorModel: Estimates error model parameters var0 (basal variance) and...
HKdata: Reverse phase protein array data of siRNA transfected cell...
logList: Logarithmize (log2) the first two RPPA list elements, i.e....
normalizeRPPA: Normalizes data in an RPPA data list
pick.high.conc: Select the highest concentration from serialy diluted samples
plotMeasurementsQC: Scatter Plots from an RPPA data
plotQC: Plot target and blank signal from RPPA control samples
plotqq: qq-plot and qq-line of an RPPA data set
plotTimeCourse: Draw time course from RPPA data
plotTimeCourseII: Multiplot function for RPPA time course datasets
read.Data: Read and Annotate RPPA rawdata
remove.arrays: Remove arrays from a RPPA data list
rppa2boxplot: Draws boxplots of groups of an RPPA data set including wilcox...
rppaList2ExpressionSet: Convert RPPA data into Expression Set
rppaList2Heatmap: Draw a heatmap with column side colors from a RPPA data
rppanalyzer-package: Read, annotate and normalize reverse phase protein array data...
S1.gpr: GenePix result files
sampledescription.old: sample description file
sampledescription.txt: sample description file
sample.median: Aggregate the replicates in an RPPA data set
select.measurements: Selects the measurement samples from an RPPA data list
select.sample.group: Selects samples from RPPA data
ser.dil.samples: Reverse phase protein array rawdata, samples serially diluted
simpleBoxplot: Draws boxplots of groups of an RPPA data set.
slidedescription.old: slide description file
slidedescription.txt: slide description file
test.correlation: Tests for correlations in RPPA data
write.Data: writes an RPPA data list into csv file

Functions

HKdata Man page
RPPanalyzer Man page
RPPanalyzer-package Man page
S1.gpr, S2.gpr, S4.gpr Man page
analyzeIntercepts Man page Source code
as.my Man page Source code
averageData Man page Source code
calcLinear Man page
calcLogistic Man page
calcSdc Man page
correctBG Man page
correctDilinterc Man page Source code
createColumnIndices Source code
curvePredictSigmoid Man page
dataI Man page
dataII Man page
dataIII Man page
dataPreproc Man page Source code
getBlocks Source code
getErrorModel Man page Source code
getIntercepts Man page Source code
getSignals Man page Source code
logList Man page Source code
normalizeRPPA Man page Source code
pick.high.conc Man page
plotHeatmap Source code
plotMeasurementsQC Man page
plotQC Man page
plotTimeCourse Man page
plotTimeCourseII Man page Source code
plotqq Man page
read.Data Man page
remove.arrays Man page
rppa2boxplot Man page Source code
rppaList2ExpressionSet Man page
rppaList2Heatmap Man page
sample.median Man page
sampledescription.old Man page
sampledescription.txt Man page
select.measurements Man page
select.sample.group Man page
ser.dil.samples Man page
simpleBoxplot Man page Source code
slidedescription.old Man page
slidedescription.txt Man page
spotbyspot Source code
test.correlation Man page Source code
write.Data Man page

Files

inst
inst/extdata
inst/extdata/Slide3.gpr
inst/extdata/slidedescription.txt
inst/extdata/S1.gpr
inst/extdata/Slide2.gpr
inst/extdata/Slide1.gpr
inst/extdata/FCF_Slide.gpr
inst/extdata/S4.gpr
inst/extdata/sampledescription.txt
inst/extdata/S2.gpr
inst/doc
inst/doc/RPPanalyzer.R
inst/doc/RPPanalyzer.pdf
inst/doc/RPPanalyzer.rnw
NAMESPACE
data
data/dataII.RData
data/sampledescription.old.txt.gz
data/HKdata.RData
data/dataI.RData
data/dataIII.RData
data/ser.dil.samples.RData
data/slidedescription.old.txt.gz
R
R/rppa2boxplot.R
R/select.measurements.R
R/pick.high.conc.R
R/correctDilinterc.R
R/dataPreproc.R
R/create.ID.col.R
R/plotHeatmap.R
R/array.id.R
R/curvePredictLinear.R
R/annotate.samples.R
R/getErrorModel.R
R/rppaList2Heatmap.R
R/correctBG.R
R/plotTimeCourse.R
R/norm.BCA.R
R/sample.median.R
R/sub.ID.R
R/heatmapcolors.R
R/protein.con.R
R/calcLinear.R
R/samples.id.R
R/rppaList2ExpressionSet.R
R/simpleBoxplot.R
R/spotbyspot.R
R/plotMeasurementsQC.R
R/get.Splines.R
R/remove.arrays.R
R/median.raw.R
R/calcLogistic.R
R/norm.texas.R
R/read.sampledescription.R
R/normalizeRPPA.R
R/annotate.arrays.R
R/test.correlation.R
R/createColumnIndices.R
R/read.Data.R
R/curveFitSigmoid.R
R/norm.static.II.R
R/dil.ser.id.R
R/logList.R
R/curvePredictSigmoid.R
R/g.link.R
R/Sips.R
R/select.sample.group.R
R/read.gpr.R
R/write.Data.R
R/curveFitLinear.R
R/norm.static.I.R
R/calcSdc.R
R/averageData.R
R/read.slidedescription.R
R/plotqq.R
R/plotQC.R
R/slides.id.R
R/plotTimeCourseII.R
R/plotDilutionSeries.R
vignettes
vignettes/workflow_RPPanalyzer.png
vignettes/papers_RPPanalyzer.bib
vignettes/Figure1.png
vignettes/b2-clj4700dn-p2
vignettes/RPPanalyzer.rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/logList.Rd
man/sampledescription.txt.Rd
man/rppanalyzer-package.Rd
man/write.Data.Rd
man/pick.high.conc.Rd
man/sample.median.Rd
man/read.Data.Rd
man/remove.arrays.Rd
man/slidedescription.txt.Rd
man/rppaList2ExpressionSet.Rd
man/getErrorModel.Rd
man/dataIII.Rd
man/averageData.Rd
man/correctDilinterc.Rd
man/slidedescription.old.Rd
man/HKdata.Rd
man/plotTimeCourse.Rd
man/correctBG.Rd
man/calcSdc.Rd
man/select.measurements.Rd
man/plotQC.Rd
man/select.sample.group.Rd
man/curvePredictSigmoid.Rd
man/dataII.Rd
man/dataI.Rd
man/calcLogistic.Rd
man/sampledescription.old.Rd
man/dataPreproc.Rd
man/rppa2boxplot.Rd
man/test.correlation.Rd
man/plotTimeCourseII.Rd
man/ser.dil.samples.Rd
man/simpleBoxplot.Rd
man/plotMeasurementsQC.Rd
man/rppaList2Heatmap.Rd
man/plotqq.Rd
man/S1.gpr.Rd
man/calcLinear.Rd
man/normalizeRPPA.Rd
RPPanalyzer documentation built on May 19, 2017, 10:32 a.m.