extract_feature_intensity: Extract intensities of specific features from a single...

In szymczak-lab/preprocessHighResMS: Preprocessing of spectra data from high resolution mass spectrometry

Description

For each of the given features local maxima will be identified in a region of 2ppm around the theoretical mz value using the algorithm implemented in the function locate.peaks. The intensity value at the local maximum with maximal intenstity within 1ppm will be extracted. If no peak could be detected, the intensity at the closest measured mz value is used.

Usage

extract_feature_intensity(
  spectrum.file,
  scanrange = c(1, 1),
  info.features,
  ppm = 10,
  num.pts = 5,
  oneside.min = 1,
  verbose = TRUE,
  res.dir = NULL
)

Arguments

spectrum.file	Character. Name of mzML file to read.
scanrange	Numeric vector of length 2. Scan range to read (see xcmsRaw).
info.features	data.frame with information about features (e.g. as generated by the function chem_formula_2_adducts).
ppm	Numeric. Resolution of mass spectrometer.
num.pts	Numeric. Minimum number of points needed to search for a peak (see locate.peaks).
oneside.min	Numeric. Minimum number of points needed on each side of the local maximum (see locate.peaks).
verbose	Logical. Print out additional information.
res.dir	Character. Name of directory where result is saved as RDS object (using the basename of the spectrum file). If NULL, a data.frame with the results will be returned.

Value

if res.dir = NULL, data frame with information for each feature:

• id: feature identifier (corresponds to chemical.form.isotope in info.features)

• mz.th: theoretical mz value

• intensity: extracted intensity

• mz.meas: mz value at center of peak (or closest measured mz value)

• peak.detected: 0 = no peak detected, 1 = peak detected, NA = no or not enough mz values available for feature

Examples

data("info.features")
res.dir = tempdir()
mzml.file = system.file("extdata",
                        "20121015b__002__07__ME.mzML",
                        package = "preprocessHighResMS")

extract_feature_intensity(spectrum.file = mzml.file,
                          scanrange = c(1, 2),
                          info.features = info.features,
                          ppm = 20,
                          res.dir = res.dir)

szymczak-lab/preprocessHighResMS documentation built on Oct. 6, 2020, 12:50 a.m.