pmp

DOI: 10.18129/B9.bioc.pmp  

Peak Matrix Processing and signal batch correction for metabolomics datasets

Bioconductor version: Release (3.16)

Methods and tools for (pre-)processing of metabolomics datasets (i.e. peak matrices), including filtering, normalisation, missing value imputation, scaling, and signal drift and batch effect correction methods. Filtering methods are based on: the fraction of missing values (across samples or features); Relative Standard Deviation (RSD) calculated from the Quality Control (QC) samples; the blank samples. Normalisation methods include Probabilistic Quotient Normalisation (PQN) and normalisation to total signal intensity. A unified user interface for several commonly used missing value imputation algorithms is also provided. Supported methods are: k-nearest neighbours (knn), random forests (rf), Bayesian PCA missing value estimator (bpca), mean or median value of the given feature and a constant small value. The generalised logarithm (glog) transformation algorithm is available to stabilise the variance across low and high intensity mass spectral features. Finally, this package provides an implementation of the Quality Control-Robust Spline Correction (QCRSC) algorithm for signal drift and batch effect correction of mass spectrometry-based datasets.

Author: Andris Jankevics [aut], Gavin Rhys Lloyd [aut, cre], Ralf Johannes Maria Weber [aut]

Maintainer: Gavin Rhys Lloyd <g.r.lloyd at bham.ac.uk>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("pmp")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("pmp")

 

HTML	R Script	Peak Matrix Processing for metabolomics datasets
HTML	R Script	Signal drift and batch effect correction and mass spectral quality assessment
HTML	R Script	Signal drift and batch effect correction for mass spectrometry
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, MassSpectrometry, Metabolomics, QualityControl, Software
Version	1.10.0
In Bioconductor since	BioC 3.11 (R-4.0) (3 years)
License	GPL-3
Depends	R (>= 4.0)
Imports	stats, impute, pcaMethods, missForest, ggplot2, methods, SummarizedExperiment, S4Vectors, matrixStats, grDevices, reshape2, utils
LinkingTo
Suggests	testthat, covr, knitr, rmarkdown, BiocStyle, gridExtra, magick
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	metabolomicsWorkbenchR, structToolbox
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	pmp_1.10.0.tar.gz
Windows Binary	pmp_1.10.0.zip
macOS Binary (x86_64)	pmp_1.10.0.tgz
macOS Binary (arm64)	pmp_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pmp
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pmp
Bioc Package Browser	https://code.bioconductor.org/browse/pmp/
Package Short Url	https://bioconductor.org/packages/pmp/
Package Downloads Report	Download Stats