MSnbase: removeNoId-methods – R documentation

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removeNoId-methods

Removes non-identified features

Description

The method removes non-identifed features in MSnExp and MSnSet instances using relevant information from the feaureData slot of a user-provide filtering vector of logicals.

Methods

signature(object = "MSnExp", fcol = "pepseq", keep = NULL): Removes the feature from object that have a feature fcol (default is "pepseq") equal to NA. Alternatively, one can also manually define keep, a vector of logical, defining the feature to be retained.
signature(object = "MSnSet", fcol = "pepseq", keep = NULL): As above of MSnSet instances.

Author(s)

Laurent Gatto <lg390@cam.ac.uk>

Examples

quantFile <- dir(system.file(package = "MSnbase", dir = "extdata"),
                     full.name = TRUE, pattern = "mzXML$")
  identFile <- dir(system.file(package = "MSnbase", dir = "extdata"),
                     full.name = TRUE, pattern = "dummyiTRAQ.mzid")
  msexp <- readMSData(quantFile)
  msexp <- addIdentificationData(msexp, identFile)
  fData(msexp)$sequence
  length(msexp)

  ## using default fcol
  msexp2 <- removeNoId(msexp)
  length(msexp2)
  fData(msexp2)$sequence

  ## using keep
  print(fvarLabels(msexp))
  (k <- fData(msexp)$'MS.GF.EValue' > 75)
  k[is.na(k)] <- FALSE
  k
  msexp3 <- removeNoId(msexp, keep = k)
  length(msexp3)
  fData(msexp3)$sequence

MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics

v2.16.1

Artistic-2.0

Authors

Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker and Lieven Clement.

Initial release