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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 |