dot-cleanRawPDTMT: Clean raw TMT data from Proteome Discoverer

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

Clean raw TMT data from Proteome Discoverer

Description

Clean raw TMT data from Proteome Discoverer

Usage

.cleanRawPDTMT(
  msstats_object,
  remove_shared = TRUE,
  remove_protein_groups = TRUE,
  protein_id_column = "ProteinAccessions",
  intensity_columns_regexp = "Abundance"
)

Arguments

msstats_object	an object of class MSstatsSpectroMineFiles.
remove_shared	lgl, if TRUE, shared peptides will be removed.
remove_protein_groups	if TRUE, proteins with numProteins > 1 will be removed.
protein_id_column	chr, name of a column with protein IDs.
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 Dec. 17, 2024, 1:14 a.m.