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inst 040000
man 040000
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vignettes 040000
.Rbuildignore 100644 0 kb
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DESCRIPTION 100644 2 kb
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# MQmetrics <!-- badges: start --> <!-- badges: end --> MQmetrics serves as a tool to analyze the quality of the proteomics data coming from the LC-MS/MS. As input, it takes the directory to the files resulting from a MaxQuant analysis and returns a pdf with diverse parameters. ## Installation You can install the stable version of MQmetrics from Biocodunctor with: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("MQmetrics") ``` I highly advice to install the development version from bioconductor since it contains several updates (check the news). ``` r BiocManager::install("MQmetrics", version = 'devel') ``` You can also install the latest version from [GitHub]( if you know what you are doing with: ``` r # install.packages("devtools") devtools::install_github("svalvaro/MQmetrics") ``` ## Example MQmetrics it’s easy to use, and will provide you information about your Proteomics MaxQuant analysis. Start by loading the library. By default, the MaxQuant results will be stored in a folder named *Combined*. The directory to that folder is all you need to use MQmetrics. ``` r library(MQmetrics) MQPathCombined <- "D:/Documents/MaxQuant_results/example5/combined/" # Use forward slashes in both windows/or linux. MQPathCombined <- "/home/alvaro/Documents/MaxQuant/example5/combined/" ``` The main function of the package is `generateReport()`. It will generate a PDF report containing several visualizations and tables from different MaxQuant output tables. As input it is only necessary to provide the Path to the *Combined* folder of MaxQuant output. ``` r generateReport(MQPathCombined, long_names = TRUE, sep_names = '_') ``` Two useful parameters of every function including `generateReport()` are: *long\_names* and *sep\_names*. They will allow a clear visualization of those samples that have long names separated by a character. In this example, the Experiment names are one full string separated by underscores (\_): *PLK010\_QC02\_210121\_HeLa\_125ng\_150meth*. ``` r # make_MQCombined reads all the files needed from the MaxQuant output and # remove Potential contaminants, reverse, and proteins identified by site only. MQCombined <- make_MQCombined(MQPathCombined, remove_contaminants = TRUE) PlotIntensity(MQCombined, long_names = TRUE, sep_names = '_') ``` <img src="man/figures/README-example_long_names-1.png" width="100%" /> Check the [vignettes]( for more information.