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 (3.19)
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>
citation("pmp")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("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
Reference Manual |
Details
biocViews | BatchEffect, MassSpectrometry, Metabolomics, QualityControl, Software |
Version | 1.15.1 |
In Bioconductor since | BioC 3.11 (R-4.0) (4 years) |
License | GPL-3 |
Depends | R (>= 4.0) |
Imports | stats, impute, pcaMethods, missForest, ggplot2, methods, SummarizedExperiment, S4Vectors, matrixStats, grDevices, reshape2, utils |
System Requirements | |
URL |
See More
Suggests | testthat, covr, knitr, rmarkdown, BiocStyle, gridExtra, magick |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | metabolomicsWorkbenchR, structToolbox |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | |
Windows Binary | |
macOS Binary (x86_64) | |
macOS Binary (arm64) | |
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/ |
Package Downloads Report | Download Stats |