This is the development version of limpa; for the stable release version, see limpa.
Quantification and Differential Analysis of Proteomics DataBioconductor version: Development (3.22)
Quantification and differential analysis of mass-spectrometry proteomics data, with probabilistic recovery of information from missing values. Estimates the detection probability curve (DPC), which relates the probability of successful detection to the underlying expression level of each peptide, and uses it to incorporate peptide missing values into protein quantification and into subsequent differential expression analyses. The package produces objects suitable for downstream analysis in limma. The package accepts peptide-level data with missing values and produces complete protein quantifications without missing values. The uncertainty introduced by missing value imputation is propagated through to the limma analyses using variance modeling and precision weights. The package name "limpa" is an acronym for "Linear Models for Proteomics Data".
Author: Mengbo Li [aut] ORCID: 0000-0002-9666-5810 , Gordon Smyth [cre, aut] ORCID: 0000-0001-9221-2892
Maintainer: Gordon Smyth <smyth at wehi.edu.au>
Citation (from within R, entercitation("limpa")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("limpa")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("limpa")Follow Installation instructions to use this package in your R session.
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