msNormStandard: Normalisation by standards

In flajole/MSdata: Mass-spectrometry data analysis package

Description

Normalisation by the list of external or internal standards. The list of the standards is provided as a file with three columns: compound, m/z, retention time. By these MZ and RT values corresponding peaks in dataset are determined and their sum intensity is used for normalisation.
Afterwards, standards are excluded from feature list.

Usage

## S4 method for signature 'MSdata'
msNormStandard(msdata, standards.list, mzwindow = 0.01,
  rtwindow = 10, meanInt = 2000, recalculateMean = FALSE)

Arguments

msdata	MSdata-class object
standards.list	The link to the file with the table of standards looking like: compound, m/z, retention time
mzwindow	Range (in ppm) for searching the peak corresponding to a standard from the list.
rtwindow	Range (in seconds) for searching the peak corresponding to a standard from the list.
meanInt	Mean sum intensity of all the standards (usually, got from previous experiments).
recalculateMean	If TRUE then meanInt is not used, but is recalculated from these particular data.

Value

MSdata-class object with normalised intensity matrix

See Also

msNorm, msNormBiomass, msScaling, msTransform

flajole/MSdata documentation built on May 16, 2019, 1:17 p.m.