rollup_pep2prot: wrapper function for peptide-to-protein rollup

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

wrapper function for peptide-to-protein rollup

Description

converts a table with peptide-level abundance values to protein-level data by combining data from respective peptides per protein (per sample).

Usage

rollup_pep2prot(
  tib,
  intensity_is_log2 = TRUE,
  rollup_algorithm,
  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
rollup_algorithm	algorithm for combining peptides to proteins. Options: 'maxlfq', 'sum', 'tukey_median'. The former applies the MaxLFQ algorithm, the second employs the 'classic' strategy of summing all peptides per protein (non-log values), the latter uses Tukey's median polish algorithm. Alternatively, one can specify "maxlfq_diann" to use the DIA-NN R package's implementation for MaxLFQ instead of the faster implementation from the iq R package (default when using 'maxlfq')
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.