getPeptideInfo: get peptide information from the peptide table from a...

In BenBruyneel/proteinDiscover: ProteinDiscover

get peptide information from the peptide table from a pdResult file based on the provided proteinAccession (uniprot) codes. Raw columns are "translated"

Description

get peptide information from the peptide table from a pdResult file based on the provided proteinAccession (uniprot) codes. Raw columns are "translated"

Usage

getPeptideInfo(
  db,
  columns = "AbundancesNormalized",
  addStandardColumns = TRUE,
  proteinAccessions = knockOutProteins()$Accession,
  removeUnusedQuantInfo = TRUE
)

Arguments

db	database access 'handle'
columns	allows the selection of columns to take from the table. The columns: PeptideGroupID, Sequence, Modifications, QuanInfo are automatically included. Default column to be retrieved is AbundancesNormalized
addStandardColumns	if TRUE then the following columns are added by default to the columnNames argument: "PeptideGroupID", "Sequence", "Modifications" & "QuanInfo". Please note that this will give problems if these columns are also in the columnNames argument. Also: to be able to use the argument removeUnusedQuantInfo = TRUE, you MUST retrieve the "QuantInfo" column
proteinAccessions	defines from which protein(s) info will be retrieved (character vector)
removeUnusedQuantInfo	default = TRUE. IF TRUE then only peptide info rows with NA as QuantInfo are kept (the others contain problematic abundance info or none at all)

Value

a named list of data.frames (the names are the proteinAccessions)

Note

this function uses the default getProteinInfoRaw function. If more control over the "translation" of raw columns is needed, then use getPeptideInfoRaw and do the translation manually

BenBruyneel/proteinDiscover documentation built on March 16, 2024, 4:36 p.m.