qPLEXanalyzer-package {qPLEXanalyzer} | R Documentation

## Tools for qPLEX-RIME data analysis

### Description

Tools for quantitiative proteomics data analysis generated from qPLEX-RIME method

### Details

Package: | qPLEXanalyzer
Type: | Package
Version: | 1.0.0
Date: | 2018-04-23
License: | GPL
Depends: | methods

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

- intensityPlot: Intensity distribution plot of all the samples

- intensityBoxplot: Intensity distribution boxplot of all the samples

- peptideIntensityPlot: Peptide intensity distribution plot of specific protein

- pcaPlot: PCA plot of all the samples

- maVolPlot: MA or Volcano plot of differential analysis results

- corrPlot: Correlation plot of all the samples

- rliPlot: Relative intensity plot of all the samples

- hierarchicalPlot: Hierarchical clustering plot of all the samples

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

- coveragePlot: Computes and display protein sequence coverage of selected protein in proteomics experiment

### Author(s)

Matthew Eldridge, Kamal Kishore, Ashley Sawle (Maintainer)

ads2202cu@gmail.com

[Package qPLEXanalyzer version 1.6.0 Index]