A toolkit for analyzing multiplexed proteomics data with an emphasis on finding a reliability threshold and accounting for signal dependent heteroskedactity.
devtools::install_github("https://github.com/calico/msTrawler")
- clone or pull repo
git clone git@github.com:calico/msTrawler.git
- cd to parent directory
cd ~/workspace
- install with
--no-staged-installflag
R CMD INSTALL msTrawler --no-staged-install
the --no-staged-install option is essential, otherwise will not build.
- test in RStudio
library(msTrawler)
4. test converting proteome discoverer ouput to R dataframe
setwd("/PATH/TO/LIBRARY/FOLDER") df <- convertPdFile("data/pd_example_export_PSMs.txt", "data/pd_example_export_Proteins.txt")
5. For help using the package please see the tutorial here
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https://github.com/calico/msTrawler/blob/main/msTrawler_tutorial.pdf
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