MSstatsLOBD

DOI: 10.18129/B9.bioc.MSstatsLOBD    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see MSstatsLOBD.

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

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	LOB/LOD Estimation Workflow
PDF		Reference Manual

Details

biocViews	DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel
Version	1.0.0
In Bioconductor since	BioC 3.13 (R-4.1) (< 6 months)
License	Artistic-2.0
Depends	R (>= 4.0)
Imports	minpack.lm, ggplot2, utils, stats, grDevices
LinkingTo	Rcpp
Suggests	BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr
SystemRequirements
Enhances
URL
BugReports	https://github.com/Vitek-Lab/MSstatsLODQ/issues
Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package	MSstatsLOBD_1.0.0.tar.gz
Windows Binary	MSstatsLOBD_1.0.0.zip
macOS 10.13 (High Sierra)	MSstatsLOBD_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MSstatsLOBD
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MSstatsLOBD
Package Short Url	https://bioconductor.org/packages/MSstatsLOBD/
Package Downloads Report	Download Stats