proteomics: Statistical Analysis of High Throughput Proteomics Data
Version 0.2

Provides methods for making inference in isobaric labelled LC-MS/MS experiments, i.e. iTRAQ experiments. It provides a function that reasonably parses a CSV-export from Proteome Discoverer(TM) into a data frame that can be easily handled in R. Functions and methods are provided for quality control, filtering, norming, and the calculation of response variables for further analysis. The merging of multiple iTRAQ experiments with respect to a reference is also covered.

AuthorThomas W. D. Möbius <kontakt@thomasmoebius.de>
Date of publication2014-11-22 01:30:39
MaintainerThomas W. D. Möbius <kontakt@thomasmoebius.de>
LicenseGPL-3
Version0.2
URL http://00tau.github.io/proteomics-in-r/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("proteomics")

Popular man pages

addIonSatistics: Summary statistics - Ion intensities per spectra
addRetentionAtApex: Summary statistics - Calculates retention time statistics at...
adjustBy: Adjust for confounding - Generic function for centring data
copyLoadings: Adjust for confounding - copy loadings from one experiment to...
pRetention: Plot Retention Time Statistics
pVolcano: Volcano plot
toProportions: Transformation - From intensity scales to density histrograms
See all...

All man pages Function index File listing

Man pages

accum: Response calculation
addIonSatistics: Summary statistics - Ion intensities per spectra
addLoadings: Adjust for confounding - add an appropiate target
addRetentionAtApex: Summary statistics - Calculates retention time statistics at...
addRetentionIndexTimeStatistics: Summary statistics - Calculates index retention time...
adjustBy: Adjust for confounding - Generic function for centring data
adjusting: Adjust for confounding - State of the art adjustments for...
adjustOne: Adjust for confounding - In one single experiment only
avrgLoading: Adjust for confounding - calculates the average loading
channelResponses: Response calculation
copyLoadings: Adjust for confounding - copy loadings from one experiment to...
factoring: Sample design - Generating multiple factor designs from...
meetSelection: Data parsing - from Proteom Discover v1.4
mergeFrames: Merging multiple experiments
norm2Reference: Response calculation
pAction: Plotting p-value distributions
plotMePeptide: Plot interaction plots of peptides
plotMeProtein: Plot interaction plots of proteins
pRetention: Plot Retention Time Statistics
pVioline: Plot Retention Time Statistics in violine form
pVolcano: Volcano plot
responseStatisics: Summary statistics - Generic to calculate summary statistics
selectByConfidence: Result filtering - Test for biological effect
selectByEffect: Result filtering - Test for biological effect
selectByFDR: Result filtering
testForPeptideEffect: Data Analysis - Testing on peptide level
testForProteinEffect: Data Analysis - Testing on protein level
testing: Data Analysis - Testing features with Tukey Honest...
testingOneshot: Data Analysis - Testing one feature without Tukey Honest...
testingTukey: Data Analysis - Testing one feature with Tukey Honest...
toAlpha: Measuring stability - angle of loading vector
toProportions: Transformation - From intensity scales to density histrograms

Functions

accum Man page Source code
addIonSatistics Man page Source code
addLoadings Man page Source code
addRetentionAtApex Man page Source code
addRetentionIndexTimeStatistics Man page Source code
adjustBy Man page Source code
adjustOne Man page Source code
adjusting Man page Source code
alpha Source code
attachModifications Source code
avrgLoading Man page Source code
avrgLoadingCalculation Source code
barcoding Source code
channelResponses Man page Source code
copyLoadings Man page Source code
extractModifications Source code
factoring Man page Source code
listModifications Source code
meetSelection Man page Source code
mergeFrames Man page Source code
norm2Reference Man page Source code
pAction Man page Source code
pRetention Man page Source code
pVioline Man page Source code
pVolcano Man page Source code
plotMePeptide Man page Source code
plotMeProtein Man page Source code
reject Source code
responseStatisics Man page Source code
selectByConfidence Man page Source code
selectByEffect Man page Source code
selectByFDR Man page Source code
testForPeptideEffect Man page Source code
testForProteinEffect Man page Source code
testing Man page Source code
testingOneshot Man page Source code
testingTukey Man page Source code
testingWithTukey Source code
toAlpha Man page Source code
toPeptide Source code
toProportions Man page Source code

Files

NAMESPACE
R
R/data-03-analysis.r
R/data-00-selection-from-PD.r
R/data-01-consolidation.r
R/zzz.R
R/data-02-merging.r
MD5
DESCRIPTION
man
man/addRetentionIndexTimeStatistics.Rd
man/pVioline.Rd
man/selectByFDR.Rd
man/copyLoadings.Rd
man/testing.Rd
man/plotMeProtein.Rd
man/toProportions.Rd
man/norm2Reference.Rd
man/pRetention.Rd
man/mergeFrames.Rd
man/testForPeptideEffect.Rd
man/selectByConfidence.Rd
man/adjustOne.Rd
man/adjusting.Rd
man/testForProteinEffect.Rd
man/toAlpha.Rd
man/addIonSatistics.Rd
man/channelResponses.Rd
man/responseStatisics.Rd
man/pAction.Rd
man/selectByEffect.Rd
man/testingTukey.Rd
man/testingOneshot.Rd
man/pVolcano.Rd
man/avrgLoading.Rd
man/factoring.Rd
man/addRetentionAtApex.Rd
man/accum.Rd
man/plotMePeptide.Rd
man/addLoadings.Rd
man/meetSelection.Rd
man/adjustBy.Rd
proteomics documentation built on May 19, 2017, 9:35 p.m.

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