alecksphillips / runmaxlfq

Simple script for applying MaxLFQ algorithm post-hoc to MaxQuant output

RunMaxLFQ

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

Requirements

CRAN Packages

• data.table
• bit64
• fst
• progress
• pbapply
• parallel
• iq

Github R Packages

• diann

Usage

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>