Welcome to the new bioconductor.org!

MSstatsLOBD

Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)


Bioconductor version: Release (3.18)

The MSstatsLOBD package allows calculation and visualization of limit of blac (LOB) and limit of detection (LOD). We define the LOB as the highest apparent concentration of a peptide expected when replicates of a blank sample containing no peptides are measured. The LOD is defined as the measured concentration value for which the probability of falsely claiming the absence of a peptide in the sample is 0.05, given a probability 0.05 of falsely claiming its presence. These functionalities were previously a part of the MSstats package. The methodology is described in Galitzine (2018) .

Author: Devon Kohler [aut, cre], Mateusz Staniak [aut], Cyril Galitzine [aut], Meena Choi [aut], Olga Vitek [aut]

Maintainer: Devon Kohler <kohler.d at northeastern.edu>

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

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("MSstatsLOBD")

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("MSstatsLOBD")
LOB/LOD Estimation Workflow HTML R Script
Reference Manual PDF

Details

biocViews DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License Artistic-2.0
Depends R (>= 4.0)
Imports minpack.lm, ggplot2, utils, stats, grDevices
System Requirements
URL
Bug Reports https://github.com/Vitek-Lab/MSstatsLODQ/issues
See More
Suggests BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package MSstatsLOBD_1.10.0.tar.gz
Windows Binary MSstatsLOBD_1.10.0.zip (64-bit only)
macOS Binary (x86_64) MSstatsLOBD_1.10.0.tgz
macOS Binary (arm64) MSstatsLOBD_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MSstatsLOBD
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MSstatsLOBD
Bioc Package Browser https://code.bioconductor.org/browse/MSstatsLOBD/
Package Short Url https://bioconductor.org/packages/MSstatsLOBD/
Package Downloads Report Download Stats