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.
|Author||Thomas W. D. Möbius <firstname.lastname@example.org>|
|Date of publication||2014-11-22 01:30:39|
|Maintainer||Thomas W. D. Möbius <email@example.com>|
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