Package: pmp
Type: Package
Title: Peak Matrix Processing and signal batch correction for
        metabolomics datasets
Version: 1.22.1
Authors@R: c(
    person(
        c("Andris"),
          "Jankevics",
           role=c("aut"),
           email="a.jankevics@bham.ac.uk"),
    person(
        c("Gavin","Rhys"),
          "Lloyd",
           role=c("aut","cre"),
           email="g.r.lloyd@bham.ac.uk"),
    person(
        c("Ralf","Johannes", "Maria"),
          "Weber",
           role=c("aut"),
           email="r.j.weber@bham.ac.uk")
    )
Maintainer@R: c( person( c("Gavin","Rhys"), "Lloyd",
        role=c("aut","cre"), email="g.r.lloyd@bham.ac.uk") )
Description: 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.
License: GPL-3
biocViews: MassSpectrometry, Metabolomics, Software, QualityControl,
        BatchEffect
Depends: R (>= 4.0)
Imports: stats, impute, pcaMethods, missForest, ggplot2, methods,
        SummarizedExperiment, S4Vectors, matrixStats, grDevices,
        reshape2, utils
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Suggests: testthat, covr, knitr, rmarkdown, BiocStyle, gridExtra,
        magick
VignetteBuilder: knitr
Collate: 'checkPeakMatrix.R' 'utils.R' 'data.R' 'filters.R'
        'glog_transformation.R' 'mv_imputation.R' 'normalisation.R'
        'sbc_main.R' 'sbc_methods.R' 'sbc_plot.R'
Config/pak/sysreqs: libicu-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-11-11 08:32:00 UTC
RemoteUrl: https://github.com/bioc/pmp
RemoteRef: RELEASE_3_22
RemoteSha: e158437407223184f635260ad848477b24004e7e
NeedsCompilation: no
Packaged: 2025-11-14 05:12:28 UTC; root
Author: Andris Jankevics [aut],
  Gavin Rhys Lloyd [aut, cre],
  Ralf Johannes Maria Weber [aut]
Maintainer: Gavin Rhys Lloyd <g.r.lloyd@bham.ac.uk>
Built: R 4.5.2; ; 2025-11-14 05:15:04 UTC; windows
