MSstatsLOBD
Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)
Bioconductor version: Release (3.19)
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("MSstatsLOBD")
):
Installation
To install this package, start R (version "4.4") 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 |
Details
biocViews | DifferentialExpression, ImmunoOncology, MassSpectrometry, Normalization, OneChannel, Proteomics, QualityControl, Software, TwoChannel |
Version | 1.12.0 |
In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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_1.12.0.tar.gz |
Windows Binary | MSstatsLOBD_1.12.0.zip (64-bit only) |
macOS Binary (x86_64) | MSstatsLOBD_1.12.0.tgz |
macOS Binary (arm64) | MSstatsLOBD_1.12.0.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 |