getPeptideProteinWeights: Get PSM-protein weights for summarization with shared...

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

Get PSM-protein weights for summarization with shared peptides

Description

Get PSM-protein weights for summarization with shared peptides

Usage

getPeptideProteinWeights(
  feature_data,
  norm = "p_norm",
  norm_parameter = 1,
  weights_mode = "contributions",
  weights_penalty = FALSE,
  weights_penalty_param = 0.1
)

Arguments

feature_data	data.table in MSstatsTMT format. See also the Details section
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.
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

Value

data.table

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