wrProteo: Proteomics Data Analysis Functions

Data analysis of proteomics experiments by mass spectrometry is supported by this collection of functions mostly dedicated to the analysis of (bottom-up) quantitative (XIC) data. Fasta-formatted proteomes (eg from Uniprot) can be read with automatic parsing and multiple annotation types (like species origin, abbreviated gene names, etc) extracted. Quantitative proteomics measurements frequently contain multiple NA values, due to physical absence of given peptides in some samples, limitations in sensitivity or other reasons. The functions provided here help to inspect graphically the data to investigate the nature of NA-values via their respective replicate measurements and to help/confirm the choice of NA-replacement by low random values. Dedicated filtering and statistical testing using the framework of package 'limma' can be run, enhanced by multiple rounds of NA-replacements to provide robustness towards rare stochastic events. Multi-species samples, as frequently used in benchmark-tests, can be run with special options consideration separating the data into sub-groups during normalization and testing. Subsequently, ROC curves can be constructed to compare multiple analysis approaches.

Version: 1.0.0
Depends: R (≥ 3.1.0)
Imports: graphics, limma, stats, wrMisc
Suggests: fdrtool, grDevices, MASS, RColorBrewer, ROTS, readxl
Published: 2020-01-08
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger at unistra.fr>
License: GPL-3
NeedsCompilation: no
CRAN checks: wrProteo results


Reference manual: wrProteo.pdf
Package source: wrProteo_1.0.0.tar.gz
Windows binaries: r-devel: wrProteo_1.0.0.zip, r-devel-gcc8: wrProteo_1.0.0.zip, r-release: wrProteo_1.0.0.zip, r-oldrel: wrProteo_1.0.0.zip
OS X binaries: r-release: wrProteo_1.0.0.tgz, r-oldrel: wrProteo_1.0.0.tgz


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