getNetCDF: getNetCDF

In IDSL.MXP: Parser for mzML, mzXML, and netCDF Files (Mass Spectrometry Data)

getNetCDF

Description

This function returns a list of two data objects needed for the mass spectrometry data processing.

Usage

getNetCDF(MSfile)

Arguments

MSfile

name of the mass spectrometry file with .cdf extension

Value

scanTable

a dataframe of different scan properties including 'seqNum', 'msLevel', 'polarity', 'peaksCount', 'totIonCurrent', 'retentionTime', 'basePeakMZ', 'basePeakIntensity', 'collisionEnergy', 'lowMZ', 'highMZ', 'precursorScanNum', 'precursorMZ', 'precursorCharge', 'precursorIntensity', 'injectionTime', 'filterString', 'scanType', 'centroided', 'isolationWindowTargetMZ', 'isolationWindowLowerOffset', 'isolationWindowUpperOffset', 'scanWindowLowerLimit', and 'scanWindowUpperLimit'.

spectraList

a list of matrices of m/z and intensity values for each chromatogram scan

Note

‘retentionTime' column in the 'scanTable’ object is presented in minute.

IDSL.MXP documentation built on March 31, 2023, 9:02 p.m.