limpca

An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family of methods


Bioconductor version: Release (3.19)

This package has for objectives to provide a method to make Linear Models for high-dimensional designed data. limpca applies a GLM (General Linear Model) version of ASCA and APCA to analyse multivariate sample profiles generated by an experimental design. ASCA/APCA provide powerful visualization tools for multivariate structures in the space of each effect of the statistical model linked to the experimental design and contrarily to MANOVA, it can deal with mutlivariate datasets having more variables than observations. This method can handle unbalanced design.

Author: Bernadette Govaerts [aut, ths], Sebastien Franceschini [ctb], Robin van Oirbeek [ctb], Michel Thiel [aut], Pascal de Tullio [dtc], Manon Martin [aut, cre] , Nadia Benaiche [ctb]

Maintainer: Manon Martin <manon.martin at uclouvain.be>

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

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("limpca")

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("limpca")
Analysis of the Trout dataset with limpca HTML R Script
Analysis of the UCH dataset with limpca HTML R Script
Get started with limpca HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ExperimentalDesign, GeneExpression, Metabolomics, MultipleComparison, PrincipalComponent, Regression, Software, StatisticalMethod, Visualization
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License Artistic-2.0
Depends R (>= 3.5.0)
Imports ggplot2, stringr, plyr, ggrepel, reshape2, grDevices, graphics, doParallel, parallel, dplyr, tibble, tidyr, ggsci, tidyverse, methods, stats, SummarizedExperiment, S4Vectors
System Requirements
URL https://github.com/ManonMartin/limpca https://manonmartin.github.io/limpca/
Bug Reports https://github.com/ManonMartin/limpca/issues
See More
Suggests BiocStyle, pander, rmarkdown, car, gridExtra, knitr, testthat (>= 3.0.0)
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Package Archives

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

Source Package limpca_1.0.0.tar.gz
Windows Binary limpca_1.0.0.zip
macOS Binary (x86_64) limpca_1.0.0.tgz
macOS Binary (arm64) limpca_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/limpca
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/limpca
Bioc Package Browser https://code.bioconductor.org/browse/limpca/
Package Short Url https://bioconductor.org/packages/limpca/
Package Downloads Report Download Stats