MSstatsLOBD
This is the released version of MSstatsLOBD; for the devel version, see MSstatsLOBD.
Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)
Bioconductor version: Release (3.23)
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) <doi:10.1074/mcp.RA117.000322>.
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")):Devon Kohler, Mateusz Staniak, Cyril Galitzine, Meena Choi, Olga Vitek. MSstatsLOBD: Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD). doi:10.18129/B9.bioc.MSstatsLOBD, R package version 1.20.0, https://bioconductor.org/packages/MSstatsLOBD.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5.5 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, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MSstatsLOBD_1.20.0.tar.gz |
| Windows Binary (x86_64) | MSstatsLOBD_1.20.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | MSstatsLOBD_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | MSstatsLOBD_1.20.0.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 |