wolski
commented
4 years ago 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
Example run script.R where LFQService processes MQanalysis and MSStats file output.