Example run scripts for MSFragger and MaxQuant. about prolfqua HOT 1 CLOSED

Before running the scripts download package and build install it.
Than set the working directory to
LFQService/inst/run_scripts

Afterwards you can either source the files with source("lfq_mixed_model_inference.R") or alternatively open it in your editor and execute it line by line.

Example of MQ ouput analysis with a factorial design can be found here:
https://github.com/wolski/LFQService/blob/master/inst/run_scripts/lfq_mixed_model_inference.R

Protein intensity level analysis using an msstats.csv file can be found here:
https://github.com/wolski/LFQService/blob/master/inst/run_scripts/emulate_msstats_ProtL.R

Peptide level analysis using an msstats.csv file can be found here:
https://github.com/wolski/LFQService/blob/master/inst/run_scripts/emulate_msstats_mixed.R

from prolfqua.