fcyu/lfqbench

Description

LFQbench^[1] is an open source R package for the automated evaluation of label-free quantification performance. The evaluation bases on the interpretation of the quantitative analysis results of hybrid proteome samples prepared in known ratios^[2].

LFQbench calculates and represents graphically a set of qualitative and quantitative performance metrics like identification rates, precision and accuracy of quantification, providing developers and end-users with a standardized set of reports to enable an in-depth performance evaluation of their software and analysis platforms.

Acknoledgement

We acknowledge to Jeremy Van der War, author of SDMTools R package, which is no longer maintained. The function auc (area under the curve) has been taken from SDMTools (under GPL license).

Installation

First, we need to install devtools:

install.packages("devtools")
library(devtools)

Then we just call

install_github("IFIproteomics/LFQbench")
library(LFQbench)

Examples

You may find a complete example on how to use LFQbench at the vignette:

vignette("LFQbench")

References

[1] Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou C, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R & Tenzer S. A multicenter study benchmarks software tools for label-free proteome quantification. Nature Biotechnology 1546-1696 (2016). DOI: 10.1038/nbt.3685

[2] Kuharev J, Navarro P, Distler U, Jahn O & Tenzer S. In-depth evaluation of software tools for data-independent acquisition based label-free quantification. Proteomics 15, 3140–3151 (2015).