Learn R Programming
⚠️There's a newer version (1.4.9) of this package.Take me there.

RPPanalyzer (version 1.4.3)

Reads, Annotates, and Normalizes Reverse Phase Protein Array Data

Description

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.

Copy Link

Version

Install

install.packages('RPPanalyzer')

Monthly Downloads

248

Version

1.4.3

License

LGPL

Maintainer

Astrid Wachter

Last Published

February 11th, 2016

Functions in RPPanalyzer (1.4.3)

S1.gpr

GenePix result files
dataI

Reverse phase protein array rawdata, samples serially diluted
correctDilinterc

Dilution series intersect correction
HKdata

Reverse phase protein array data of siRNA transfected cell line
dataII

Reverse phase protein array data, samples from a stimulation time course
calcLinear

Calculates sample concentrations using linear model fit
pick.high.conc

Select the highest concentration from serialy diluted samples
simpleBoxplot

Draws boxplots of groups of an RPPA data set.
logList

Logarithmize (log2) the first two RPPA list elements, i.e. foreground and background signal intensities
plotQC

Plot target and blank signal from RPPA control samples
select.measurements

Selects the measurement samples from an RPPA data list
rppaList2Heatmap

Draw a heatmap with column side colors from a RPPA data
sampledescription.txt

sample description file
sample.median

Aggregate the replicates in an RPPA data set
sampledescription.old

sample description file
plotTimeCourse

Draw time course from RPPA data
dataPreproc

Data preprocessing
correctBG

Corrects for background in an RPPA data set
calcLogistic

Calculates sample concentrations using sigmoid model fit
read.Data

Read and Annotate RPPA rawdata
normalizeRPPA

Normalizes data in an RPPA data list
averageData

Average biological replicates over different slides.
calcSdc

Calculates the concentration of serial diluted samples
ser.dil.samples

Reverse phase protein array rawdata, samples serially diluted
getErrorModel

Estimates error model parameters var0 (basal variance) and varR (relative variance) and produces a new data.frame with the signals and error model parameters.
plotMeasurementsQC

Scatter Plots from an RPPA data
write.Data

writes an RPPA data list into csv file
RPPanalyzer-package

Read, annotate and normalize reverse phase protein array data and get a brief overview on the biological impact.
plotTimeCourseII

Multiplot function for RPPA time course datasets
rppaList2ExpressionSet

Convert RPPA data into Expression Set
select.sample.group

Selects samples from RPPA data
plotqq

qq-plot and qq-line of an RPPA data set
slidedescription.txt

slide description file
rppa2boxplot

Draws boxplots of groups of an RPPA data set including wilcox or kruskal test.
slidedescription.old

slide description file
curvePredictSigmoid

Sigmoidal curve prediction.
remove.arrays

Remove arrays from a RPPA data list
dataIII

Reverse phase protein array data from original cancer specimen
test.correlation

Tests for correlations in RPPA data