isobar-package {isobar} | R Documentation

## Analysis and quantitation of isobarically tagged MSMS proteomics data

### Description

`isobar` provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled withOA isobaric tags, such as iTRAQ and TMT.

### Details

Package: | isobar
Version: | 1.1.2
biocViews: | Proteomics, MassSpectrometray, Bioinformatics, MultipleComparisons, QualityControl
Depends: | R (>= 2.9.0), Biobase, stats, methods, ggplot2
Imports: | distr, biomaRt
Suggests: | MSnbase,XML
LazyLoad: | yes
License: | LGPL-2
URL: | http://bioinformatics.cemm.oeaw.ac.at
Collate: | utils.R ProteinGroup-class.R IBSpectra-class.R NoiseModel-class.R ratio-methods.R sharedpep-methods.R MSnSet-methods.R zzz.R

Index:

    IBSpectra-class         IBSpectra objects
    NoiseModel-class        NoiseModel objects
    ProteinGroup-class      ProteinGroup objects
    do.log                  Log functions for IBSpectra objects
    fitCauchy               Fit weighted and unweighted Cauchy and Normal
                            distributions
    groupMemberPeptides     Peptide info for protein group members
    human.protein.names     Info on proteins
    ibspiked_set1           Isobar Data packages
    isobar-analysis         IBSpectra analysis: Protein and peptide ratio
                            calculation
    isobar-import           Loading data into IBSpectra objects using
                            readIBSpectra
    isobar-package          Analysis and quantitation of isobaric tag
                            Proteomics data
    isobar-plots            IBSpectra plots
    isobar-preprocessing    IBSpectra preprocessing
    isobar-reports          Isobar reports
    maplot.protein          MAplot for individual proteins
    number.ranges           Helper function to transform number lists to
                            ranges
    proteinInfo-methods     Methods for Function proteinInfo
    proteinRatios           protein and peptide ratios
    sanitize                Helper function for LaTeX export
    shared.ratios           Shared ratio calculation
    shared.ratios.sign      Plot and get significantly shared ratios.

Further information is available in the following vignettes:

`isobar` | Isobar Overview (source, pdf)
`isobar-devel` | Isobar for developers (source, pdf)

### Author(s)

Florian P Breitwieser <fbreitwieser@cemm.oeaw.ac.at> and Jacques Colinge <jcolinge@cemm.oeaw.ac.at>, with contributions from Xavier Robin <xavier.robin@unige.ch>

Maintainer: Florian P Breitwieser <fbreitwieser@cemm.oeaw.ac.at>

[Package isobar version 1.26.0 Index]