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)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 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_1.20.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/MSstatsLOBD/ |
| Package Short Url | https://bioconductor.org/packages/MSstatsLOBD/ |
| Package Downloads Report | Download Stats |