rollup_pep2prot_maxlfq: rollup by MaxLFQ algorithm

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

rollup by MaxLFQ algorithm

Description

Available implementations: iq R package: https://github.com/tvpham/iq/ DIA-NN R package: https://github.com/vdemichev/DiaNN/

Usage

rollup_pep2prot_maxlfq(
  tib,
  intensity_is_log2,
  implementation = "iq",
  return_as_matrix = FALSE
)

Arguments

tib	peptide tibble in long-format. missing values should be set NA, not zero. required columns: peptide_id, protein_id, sample_id, intensity
intensity_is_log2	boolean indicating if input peptide intensities are log2 scaled
implementation	implementation to use. available options: "iq", "diann"
return_as_matrix	instead of long-format tibble, return a protein*sample matrix (missing values set to NA)

ftwkoopmans/msdap documentation built on March 5, 2025, 12:15 a.m.