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Filter Spectronaut output

filter_features_sn.Rd

This function filters the precursor .txt file from Spectronaut, based on various criteria:

  1. Remove features without a master protein (PG.ProteinAccessions column)

  2. Remove features without a unique master protein

  3. Remove features matching a contaminant protein

  4. Remove features without quantification values

Usage

filter_features_sn(
  obj,
  master_protein_col = "PG.ProteinAccessions",
  unique_master = TRUE,
  filter_contaminant = TRUE,
  contaminant_proteins = NULL,
  remove_no_quant = TRUE,
  cont_string = "Cont_"
)

Arguments

obj

SummarisedExperiment containing output from Proteome Discoverer. Use readQFeatures to read in .txt file

master_protein_col

string. Name of column containing master proteins.

unique_master

logical. Filter out features without a unique master protein.

filter_contaminant

logical. Filter out features which match a contaminant protein.

contaminant_proteins

character vector. The protein IDs form the contaminant proteins

remove_no_quant

logical. Remove features with no quantification

cont_string

string. string to search for contaminants

Value

Returns a SummarisedExperiment with the filtered Proteome Discoverer output.