pmp

DOI: 10.18129/B9.bioc.pmp    

This is the development version of pmp; for the stable release version, see pmp.

Peak Matrix Processing and signal batch correction for metabolomics datasets

Bioconductor version: Development (3.12)

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 and Ralf Johannes Maria Weber

Maintainer: Andris Jankevics <a.jankevics at bham.ac.uk>

Citation (from within R, enter citation("pmp")):

Installation

To install this package, start R (version "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.0
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
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 structToolbox
Links To Me
Build Report  

Package Archives

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

Source Package pmp_1.1.0.tar.gz
Windows Binary pmp_1.1.0.zip
macOS 10.13 (High Sierra) pmp_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pmp
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pmp
Package Short Url https://bioconductor.org/packages/pmp/
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