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proteomics (version 0.2)

Statistical Analysis of High Throughput Proteomics Data

Description

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.

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Version

Install

install.packages('proteomics')

Monthly Downloads

13

Version

0.2

License

GPL-3

Maintainer

Thomas W D Mbius

Last Published

November 22nd, 2014

Functions in proteomics (0.2)

avrgLoading

Adjust for confounding -- calculates the average loading
addRetentionIndexTimeStatistics

Summary statistics -- Calculates index retention time statistics
adjustBy

Adjust for confounding -- Generic function for centring data
copyLoadings

Adjust for confounding -- copy loadings from one experiment to another
addRetentionAtApex

Summary statistics -- Calculates retention time statistics at apex
adjusting

Adjust for confounding -- State of the art adjustments for confounding
pVolcano

Volcano plot
addLoadings

Adjust for confounding -- add an appropiate target
selectByFDR

Result filtering
pVioline

Plot Retention Time Statistics in violine form
responseStatisics

Summary statistics -- Generic to calculate summary statistics
channelResponses

Response calculation
factoring

Sample design -- Generating multiple factor designs from one-dimensional factor
plotMePeptide

Plot interaction plots of peptides
meetSelection

Data parsing -- from Proteom Discover v1.4
pRetention

Plot Retention Time Statistics
testForPeptideEffect

Data Analysis -- Testing on peptide level
selectByEffect

Result filtering -- Test for biological effect
pAction

Plotting p-value distributions
toProportions

Transformation -- From intensity scales to density histrograms
selectByConfidence

Result filtering -- Test for biological effect
adjustOne

Adjust for confounding -- In one single experiment only
toAlpha

Measuring stability -- angle of loading vector
testing

Data Analysis -- Testing features with Tukey Honest Significant Differences
addIonSatistics

Summary statistics -- Ion intensities per spectra
testingTukey

Data Analysis -- Testing one feature with Tukey Honest Significant Differences
testForProteinEffect

Data Analysis -- Testing on protein level
plotMeProtein

Plot interaction plots of proteins
norm2Reference

Response calculation
accum

Response calculation
mergeFrames

Merging multiple experiments
testingOneshot

Data Analysis -- Testing one feature without Tukey Honest Significant Differences