dot-cleanRawPD: Clean raw Proteome Discoverer data

In Vitek-Lab/MSstatsConvert: Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

Clean raw Proteome Discoverer data

Description

Clean raw Proteome Discoverer data

Usage

.cleanRawPD(
  msstats_object,
  quantification_column,
  protein_id_column,
  sequence_column,
  remove_shared,
  remove_protein_groups = TRUE,
  intensity_columns_regexp = "Abundance"
)

Arguments

msstats_object	an object of class MSstatsSpectroMineFiles.
quantification_column	chr, name of a column used for quantification.
protein_id_column	chr, name of a column with protein IDs.
sequence_column	chr, name of a column with peptide sequences.
remove_shared	lgl, if TRUE, shared peptides will be removed.
remove_protein_groups	if TRUE, proteins with numProteins > 1 will be removed.
intensity_columns_regexp	regular expressions that defines intensity columns. Defaults to "Abundance", which means that columns that contain the word "Abundance" will be treated as corresponding to intensities for different channels.

Value

data.table

Vitek-Lab/MSstatsConvert documentation built on Nov. 21, 2024, 12:23 p.m.