readRaw: Read a h5 file of PTR-TOF-MS data

In camilleroquencourt/ptairMS: Pre-processing PTR-TOF-MS Data

Read a h5 file of PTR-TOF-MS data

Description

readRaw reads a h5 file with rhdf5 library, and calibrates the mass axis with mzCalibRef masses each calibrationPeriod seconds. It returns a ptrRaw-class S4 object, that contains raw data.

Usage

readRaw(
  filePath,
  calib = TRUE,
  mzCalibRef = c(21.022, 29.013424, 41.03858, 60.0525, 203.943, 330.8495),
  calibrationPeriod = 60,
  tolCalibPpm = 70,
  maxTimePoint = 900
)

Arguments

filePath	h5 absolute file path full name.
calib	boolean. If true, an external calibration is performed on the calibrationPeriod sum spectrum with mzCalibRef reference masses.
mzCalibRef	calibration parameter. Vector of exact theoretical masses values of an intensive peak without overlapping.
calibrationPeriod	in second, coefficient calibration are estimated for each sum spectrum of calibrationPeriod seconds
tolCalibPpm	calibration parameter. The maximum error tolerated in ppm. A warning appears for error greater than tolCalibPpm.
maxTimePoint	number maximal of time point to read

Value

a ptrRaw object, including slot

• rawM the data raw matrix, in count of ions

• mz the mz axis

• time time acquisition in second

Examples

library(ptairData)
filePathRaw <- system.file('extdata/exhaledAir/ind1', 'ind1-1.h5', 
package = 'ptairData')
raw <- readRaw(filePath=filePathRaw, mzCalibRef=c(21.022, 60.0525), calib=FALSE)

camilleroquencourt/ptairMS documentation built on April 24, 2024, 9:03 p.m.