readMgfData: Import mgf files as 'MSnExp' instances.

In lgatto/MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Import mgf files as 'MSnExp' instances.

Description

Reads a mgf file and generates an "MSnExp" object.

Usage

readMgfData(filename, pdata = NULL, centroided = TRUE, smoothed = FALSE,
verbose = isMSnbaseVerbose(), cache = 1)

Arguments

filename	character vector with file name to be read.
pdata	an object of class "AnnotatedDataFrame".
smoothed	Logical indicating whether spectra already smoothed or not. Default is 'FALSE'. Used to initialise "MSnProcess" object in processingData slot.
centroided	Logical indicating whether spectra are centroided or not. Default is 'TRUE'. Used to initialise "MSnProcess" object in processingData slot.
cache	Numeric indicating caching level. Default is 1. Under development.
verbose	verbosity flag.

Details

Note that when reading an mgf file, the original order of the spectra is lost. Thus, if the data was originally written to mgf from an MSnExp object using writeMgfData, although the feature names will be identical, the spectra are not as a result of the reordering. See example below.

Value

An instance of

Author(s)

Guangchuang Yu and Laurent Gatto

See Also

writeMgfData method to write the content of "Spectrum" or "MSnExp" objects to mgf files. Raw data files can also be read with the readMSData function.

Examples

  data(itraqdata)
  writeMgfData(itraqdata, con="itraqdata.mgf", COM="MSnbase itraqdata")
  itraqdata2 <- readMgfData("itraqdata.mgf")
  ## note that the order of the spectra is altered
  ## and precision of some values (precursorMz for instance)
  match(signif(precursorMz(itraqdata2),4),signif(precursorMz(itraqdata),4))
  ## [1]  1 10 11 12 13 14 15 16 17 18 ...
  ## ... but all the precursors are there
  all.equal(sort(precursorMz(itraqdata2)),
            sort(precursorMz(itraqdata)),
            check.attributes=FALSE,
            tolerance=10e-5)
  ## is TRUE
  all.equal(as.data.frame(itraqdata2[[1]]),as.data.frame(itraqdata[[1]]))
  ## is TRUE
  all.equal(as.data.frame(itraqdata2[[3]]),as.data.frame(itraqdata[[11]]))
  ## is TRUE
  f <- dir(system.file(package="MSnbase",dir="extdata"),
           full.name=TRUE,
           pattern="test.mgf")
  (x <- readMgfData(f))
  x[[2]]
  precursorMz(x[[2]])
  precursorIntensity(x[[2]])
  precursorMz(x[[1]])
  precursorIntensity(x[[1]]) ## was not in test.mgf
  scanIndex(x)

lgatto/MSnbase documentation built on Nov. 12, 2024, 10:58 a.m.