Remove features which are assigned to a protein with too few supporting features in total

For summarisation of PSM or peptide to protein, we need a minimum number of finite values per protein per sample. Where there are too few finite values for a given protein in a given sample, this function will replace all values for the protein features with NA. Proteins with too few finite values in all samples will be removed entirely.

This function is useful for Label-Free Quantification but also when using robust summarisation for isobaric tagging without PSM-level imputation

restrict_features_per_protein(
  obj,
  min_features,
  master_protein_col = "Master.Protein.Accessions",
  plot = TRUE
)

Arguments

obj

MSnSet with PSM or peptide-level quantification

min_features

numeric Threshold for minimum features per protein

master_protein_col

character Column name for master protein

plot

Set TRUE to plot histogram of features per protein per sample

Value

MSnSet