restrict_features_per_protein: Remove features which are assigned to a protein with too few...

In CambridgeCentreForProteomics/camprotR: Processing, analysing and visualising CCP proteomics data

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

Description

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

Usage

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

CambridgeCentreForProteomics/camprotR documentation built on Jan. 27, 2023, 8:36 p.m.