getSumSpectrum: Get Sum Mass Spectrum

In pmbrophy/mzDataTable: Import and convert raw mass spectrometry data formats

Description

Sum multiple scans and optionally normalize the spectrum. Scans are gridded by the grouping algorithm 'indexMasterSpectrum()'.

Usage

getSumSpectrum(
  mzObj,
  ppmTol = NULL,
  iStart = NULL,
  iStop = NULL,
  tStart = NULL,
  tStop = NULL,
  normalize = FALSE,
  method = "sqrt",
  isCentroid = TRUE
)

Arguments

mzObj	a data.table or disk.frame imported from mzML/mzXML file.
ppmTol	The mass accuracy of the instrument in ppm. Default = NULL
iStart	Optional. The integer start index to begin extracting ions. Default = NULL.
iStop	Optional. The integer stop index stop extracting ions. Default = NULL.
tStart	Optional. The numeric time value to begin extracting ions. Default = NULL.
tStop	Optional. The numeric time value to stop extracting ions. Default = NULL.
normalize	Logical. Default = 'FALSE'. Should the data be normalized?
method	the normalization method. "maxPeak", "sum", or "sqrt".
isCentroid	Logical. The default is 'TRUE'. Are the spectra centroids?

Value

Returns a data.table

pmbrophy/mzDataTable documentation built on June 6, 2020, 7:43 a.m.