Simple script for applying MaxLFQ algorithm post-hoc to MaxQuant output with option to distribute batches of protein groups across cores/cluster
Uses implementations of MaxLFQ from iq and diann
- data.table
- bit64
- fst
- progress
- pbapply
- parallel
- iq
Rscript --vanilla RunMaxLFQ.R \
<path to evidence/peptides.txt> \
<path to proteinGroups.txt, default: ./proteinGroups.txt> \
<path for output, default: ./output.txt> \
<serial/parallel, default: serial> \
<nBatches default: 1> <nWorkers, default: 1> \
<useDIANN, default: FALSE>