Clean raw Proteome Discoverer data

Clean raw Proteome Discoverer data

.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