qPLEXanalyzer-package {qPLEXanalyzer} | R Documentation

## Tools for qPLEX-RIME data analysis

### Description

Tools for quantitiative proteomics data analysis generated from qPLEX-RIME method The package offers the following functionalities Data processing, normalization & analysis:

- `convertToMSnset`: Converts quantitative data to a MSnSet

- `summarizeIntensities`: Summarizes multiple peptide measurements for a protein

- `normalizeQuantiles`: Performs quantile normalization on the peptides/proteins intensities

- `normalizeScaling`: Performs scaling normalization on the peptides/proteins intensities (mean, median or sum)

- `groupScaling`: Performs scaling normalization on the peptides/proteins intensities within group (median or mean)

- `rowScaling`: Normalization by scaling peptide/protein intensity across all samples

- `regressIntensity`: Performs linear regression on protein intensities based on selected protein

- `computeDiffStats`: Compute differential statistics for the given contrasts

- `getContrastResults`: Get differential statistics results for given contrast

Visualization:

- `assignColours`: Assigns colours to samples in groups

- `corrPlot`: Correlation plot of all the samples

- `coveragePlot`: Computes and display protein sequence coverage of

- `hierarchicalPlot`: Hierarchical clustering plot of all the samples

- `intensityBoxplot`: Intensity distribution boxplot of all the samples

- `intensityPlot`: Intensity distribution plot of all the samples

- `maVolPlot`: MA or Volcano plot of differential analysis results

- `pcaPlot`: PCA plot of all the samples

- `peptideIntensityPlot`: Peptide intensity distribution plot of specific protein

- `plotMeanVar`: Computes and plots mean-variance for samples in MSnSet

- `rliPlot`: Relative intensity plot of all the samples selected protein in proteomics experiment

### Author(s)

Matthew Eldridge, Kamal Kishore, Ashley Sawle (Maintainer)

ads2202cu@gmail.com

[Package qPLEXanalyzer version 1.10.0 Index]