MSstatsLOBD

DOI: 10.18129/B9.bioc.MSstatsLOBD    

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

Bioconductor version: Release (3.14)

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 "4.1") 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 1.2.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 years)
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
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package MSstatsLOBD_1.2.0.tar.gz
Windows Binary MSstatsLOBD_1.2.0.zip
macOS 10.13 (High Sierra) MSstatsLOBD_1.2.0.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
Old Source Packages for BioC 3.14 Source Archive

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