getWeightedSummarySingleRun: Robust summary for a single run

In Vitek-Lab/SharedPeptidesExplorer: Weighted Protein-Level Summarization for Protein Clusters

Robust summary for a single run

Description

Robust summary for a single run

Usage

getWeightedSummarySingleRun(
  feature_data,
  peptide_protein_dt,
  norm,
  norm_parameter,
  weights_mode,
  tolerance,
  max_iter,
  initial_summary,
  weights_penalty,
  weights_penalty_param
)

Arguments

feature_data	data.table in MSstatsTMT format. See also the Details section
peptide_protein_dt	table of peptide-protein matches
norm	"p_norm" or "Huber"
norm_parameter	p for norm=="p_norm", M for norm=="Huber"
weights_mode	"contributions" for "sum to one" and "non-negative" conditions, "probabilities" for only "non-negative" condition.
tolerance	tolerance to indicate weights convergence
max_iter	maximum number of iteration of the procedure
initial_summary	"unique", "flat" or "flat unique"
weights_penalty	if TRUE, weights will be penalized for deviations from equal value for all proteins matching to a given PSM
weights_penalty_param	penalty parameter

Vitek-Lab/SharedPeptidesExplorer documentation built on April 14, 2025, 1:45 p.m.