proteomics: Statistical Analysis of High Throughput Proteomics Data

Share:

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 <kontakt@thomasmoebius.de>
Date of publication
2014-11-22 01:30:39
Maintainer
Thomas W. D. Möbius <kontakt@thomasmoebius.de>
License
GPL-3
Version
0.2
URLs

View on CRAN

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

Files in this package

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