RPPanalyzer-package |
Read, annotate and normalize reverse phase protein array data and get a brief overview on the biological impact. |
analyzeIntercepts |
Dilution series intersect correction |
as.my |
Dilution series intersect correction |
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 time course |
dataIII |
Reverse phase protein array data from original cancer specimen |
dataPreproc |
Data preprocessing |
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. |
getIntercepts |
Dilution series intersect correction |
getSignals |
Dilution series intersect correction |
HKdata |
Reverse phase protein array data of siRNA transfected cell line |
logList |
Logarithmize (log2) the first two RPPA list elements, i.e. foreground and background signal intensities |
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 or kruskal test. |
rppaList2ExpressionSet |
Convert RPPA data into Expression Set |
rppaList2Heatmap |
Draw a heatmap with column side colors from a RPPA data |
RPPanalyzer |
Read, annotate and normalize reverse phase protein array data and get a brief overview on the biological impact. |
S1.gpr, S2.gpr, S4.gpr |
GenePix result files |
sample.median |
Aggregate the replicates in an RPPA data set |
sampledescription.old |
sample description file |
sampledescription.txt |
sample description file |
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 |