getXIC: Get XIC from data.table or disk.frame

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

Description

Extract ions by mz using a variety of options for subsetting. See details.

Usage

getXIC(
  mzObj,
  mz,
  mz_delta = NULL,
  ppmTol = NULL,
  iStart = NULL,
  iStop = NULL,
  tStart = NULL,
  tStop = NULL,
  normalize = FALSE,
  method = "sqrt"
)

Arguments

mzObj	a data.table or disk.frame imported from mzML/mzXML file.
mz	the m/z value to extract.
mz_delta	Optional. A numeric value +/- the mz value to extract. Default = NULL.
ppmTol	Optional. 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".

Details

mzObj and mz must be provided. Default behavior is to extract ions exactly matching mz value accross all time.

Specifying mz_delta or ppmTol will result in mz filtering. mz_delta will extract ions with values in the range where mz >= mz-mz_delta and mz <= mz+mz_delta. Specifying ppmTol workes similarly, but calculates the upper and lower bounds from ppm mass error.

Specifying iStart/iStop or tStart/tStop will result in time filtering.

Value

Returns a subset of the original mzObj as a data.table

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