Statistical Analysis of High Throughput Proteomics Data

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Documentation for package ‘proteomics’ version 0.2

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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 apex
addRetentionIndexTimeStatistics Summary statistics - Calculates index retention time statistics
adjustBy Adjust for confounding - Generic function for centring data
adjusting Adjust for confounding - State of the art adjustments for confounding
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 another
factoring Sample design - Generating multiple factor designs from one-dimensional factor
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 Significant Differences
testingOneshot Data Analysis - Testing one feature without Tukey Honest Significant Differences
testingTukey Data Analysis - Testing one feature with Tukey Honest Significant Differences
toAlpha Measuring stability - angle of loading vector
toProportions Transformation - From intensity scales to density histrograms