The goal of DiannReportGenerator is to make a new document that contains, for each sample, the "MaxLFQ Intensity" and "Number of Peptides Quantified" for every Protein Group.
Precursors are filtered by both Library Q-Value and Protein Group Library Q-Value at 0.01 and PEP of 0.5, and keratin IDs are removed. After filtering, MaxLFQ-based quantification (https://doi.org/10.1074/mcp.M113.031591) is performed. The number of precursors/peptides that were quantified within a given protein group is counted and the data is then tidied to long format where every row corresponds to a protein group (reported as the FASTA accession number) and the rows contain:
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Gene Name
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Protein Name
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MaxLFQ Intensity for each sample
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Number of Peptides for each sample
Prior to installing this package, you will need to install the latest version of RTools along with the "DiaNN R Package" developed by the Demichev lab. You can download and install RTools from here: https://cran.r-project.org/bin/windows/Rtools/
DiaNN R Package can be found here: https://github.com/vdemichev/diann-rpackage
You can install DiannReportGenerator from:
https://github.com/URMC-MSRL/DiannReportGenerator
In short, instructions are as follows:
install.packages("devtools")
devtools::install_github("https://github.com/vdemichev/diann-rpackage")
devtools::install_github("https://github.com/URMC-MSRL/DiannReportGenerator")
library(DiannReportGenerator)
library(DiannReportGenerator)
Put the name of the main DIA-NN report in quotes, followed by whatever you wish to call the new document in quotes.
diann_reporter("report.tsv",
"new_report.tsv")