Package: RPPanalyzer 1.4.9

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

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.

Authors:Heiko Mannsperger with contributions of Stephan Gade

RPPanalyzer_1.4.9.tar.gz
RPPanalyzer_1.4.9.zip(r-4.5)RPPanalyzer_1.4.9.zip(r-4.4)RPPanalyzer_1.4.9.zip(r-4.3)
RPPanalyzer_1.4.9.tgz(r-4.4-any)RPPanalyzer_1.4.9.tgz(r-4.3-any)
RPPanalyzer_1.4.9.tar.gz(r-4.5-noble)RPPanalyzer_1.4.9.tar.gz(r-4.4-noble)
RPPanalyzer_1.4.9.tgz(r-4.4-emscripten)RPPanalyzer_1.4.9.tgz(r-4.3-emscripten)
RPPanalyzer.pdf |RPPanalyzer.html✨
RPPanalyzer/json (API)

# Install 'RPPanalyzer' in R:

install.packages('RPPanalyzer', repos = c('https://sybig.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

HKdata - Reverse phase protein array data of siRNA transfected cell line
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
sampledescription.old - Sample description file
ser.dil.samples - Reverse phase protein array rawdata, samples serially diluted
slidedescription.old - Slide description file

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

28 exports 1 stars 1.85 score 82 dependencies 6 mentions 71 scripts 388 downloads

Last updated 8 months agofrom:1bf858e340. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 24 2024
R-4.5-win	OK	Aug 24 2024
R-4.5-linux	OK	Aug 24 2024
R-4.4-win	OK	Aug 24 2024
R-4.4-mac	OK	Aug 24 2024
R-4.3-win	OK	Aug 24 2024
R-4.3-mac	OK	Aug 24 2024

Exports:averageData calcLinear calcLogistic calcSdc correctBG correctDilinterc curvePredictSigmoid dataPreproc getErrorModel logList normalizeRPPA pick.high.conc plotMeasurementsQC plotQC plotqq plotTimeCourse plotTimeCourseII read.Data remove.arrays rppa2boxplot rppaList2ExpressionSet rppaList2Heatmap sample.median select.measurements select.sample.group simpleBoxplot test.correlation write.Data

Dependencies:backports base64enc Biobase BiocGenerics bitops bslib cachem caTools checkmate cli cluster codetools colorspace data.table digest evaluate fansi farver fastmap fontawesome foreach foreign Formula fs gam ggplot2 glue gplots gridExtra gtable gtools highr Hmisc htmlTable htmltools htmlwidgets isoband iterators jquerylib jsonlite KernSmooth knitr labeling lattice lifecycle limma magrittr MASS Matrix MatrixModels memoise mgcv mime munsell nlme nnet pillar pkgconfig quantreg R6 rappdirs RColorBrewer rlang rmarkdown rpart rstudioapi sass scales SparseM statmod stringi stringr survival tibble tinytex utf8 vctrs viridis viridisLite withr xfun yaml

An R Package to read, normalize and visualize RPPA data

Rendered fromRPPanalyzer.rnwusingutils::Sweaveon Aug 24 2024.

Last update: 2017-06-26
Started: 2014-01-21

Citation

Readme and manuals

Help Manual

Help page	Topics
Read, annotate and normalize reverse phase protein array data and get a brief overview on the biological impact.	RPPanalyzer-package RPPanalyzer
Average biological replicates over different slides.	averageData
Calculates sample concentrations using linear model fit	calcLinear
Calculates sample concentrations using sigmoid model fit	calcLogistic
Calculates the concentration of serial diluted samples	calcSdc
Corrects for background in an RPPA data set	correctBG
Dilution series intersect correction	analyzeIntercepts as.my correctDilinterc getIntercepts getSignals
Sigmoidal curve prediction.	curvePredictSigmoid
Reverse phase protein array rawdata, samples serially diluted	dataI
Reverse phase protein array data, samples from a stimulation time course	dataII
Reverse phase protein array data from original cancer specimen	dataIII
Data preprocessing	dataPreproc
Estimates error model parameters var0 (basal variance) and varR (relative variance) and produces a new data.frame with the signals and error model parameters.	getErrorModel
Reverse phase protein array data of siRNA transfected cell line	HKdata
Logarithmize (log2) the first two RPPA list elements, i.e. foreground and background signal intensities	logList
Normalizes data in an RPPA data list	normalizeRPPA
Select the highest concentration from serialy diluted samples	pick.high.conc
Scatter Plots from an RPPA data	plotMeasurementsQC
Plot target and blank signal from RPPA control samples	plotQC
qq-plot and qq-line of an RPPA data set	plotqq
Draw time course from RPPA data	plotTimeCourse
Multiplot function for RPPA time course datasets	plotTimeCourseII
Read and Annotate RPPA rawdata	read.Data
Remove arrays from a RPPA data list	remove.arrays
Draws boxplots of groups of an RPPA data set including wilcox or kruskal test.	rppa2boxplot
Convert RPPA data into Expression Set	rppaList2ExpressionSet
Draw a heatmap with column side colors from a RPPA data	rppaList2Heatmap
GenePix result files	S1.gpr, S2.gpr, S4.gpr
Aggregate the replicates in an RPPA data set	sample.median
sample description file	sampledescription.old
sample description file	sampledescription.txt
Selects the measurement samples from an RPPA data list	select.measurements
Selects samples from RPPA data	select.sample.group
Reverse phase protein array rawdata, samples serially diluted	ser.dil.samples
Draws boxplots of groups of an RPPA data set.	simpleBoxplot
slide description file	slidedescription.old
slide description file	slidedescription.txt
Tests for correlations in RPPA data	test.correlation
writes an RPPA data list into csv file	write.Data