createPtrSet {ptairMS} | R Documentation

## Creates a ptrSet object form a directory

### Description

This function creates a `ptrSet-class` S4 object. It opens each file and:

- performs an external calibration by using the `mzCalibRef` reference masses on the sum spectra every `calibrationPeriod` second

- quantifies the primary ion (H3O+ isotope by default) on the average total ion spectrum.

- calculates expiration on the `mzBreathTracer` trace. The part of the trace where the intensity is higher than `fracMaxTIC * max(trace)` is considered as expiration. If `fracMaxTIC` is different to zero, this step is skipped

- defines the set of knots for the peak analysis (see `detectPeak`)

- provides a default sampleMetadata based on the tree structure of the directory and the acquisition date (a `data.frame` with file names as row names)

- If `saveDir` is not `NULL`, the returned object will be saved as a `.Rdata` in `saveDir` with the `setName` as name

### Usage

    createPtrSet(
      dir,
      setName,
      mzCalibRef = c(21.022, 29.013424, 41.03858, 60.0525, 203.943, 330.8495),
      calibrationPeriod = 60,
      fracMaxTIC = 0.8,
      mzBreathTracer = NULL,
      knotsPeriod = 3,
      mzPrimaryIon = 21.022,
      saveDir = NULL
    )

### Arguments

`dir` | character. a directory path which contains several h5 files, possibly organized in subfolder
`setName` | character. name of the ptrSet object. If 'saveDir' is not null, the object will be saved with this name.
`mzCalibRef` | vector of the reference mass values; those masses should be accurate, and the corresponding peaks should be of high intensity and 'unique' in a nominal mass interval (without overlapping peaks) to performs calibration. See `?calibration`.
`calibrationPeriod` | in second, coefficient calibration are estimated for each sum spectrum of `calibrationPeriod` seconds
`fracMaxTIC` | Fraction (between 0 and 1) of the maximum of the Total Ion Current (TIC) amplitude after baseline removal. Only the part of the spectrum where the TIC intensity is higher than 'fracMaxTIC * max(TIC) ' will be analyzed. If you want to analyze the entire spectrum, set this parameter to 0.
`mzBreathTracer` | integer: nominal mass of the Extracted Ion Current (EIC) used to compute the expiration time limits. If `NULL`, the limits will be computed on the Total Ion Current (TIC).
`knotsPeriod` | period in second (time scale) between two knots for the two dimensional modeling
`mzPrimaryIon` | Exact mass of the primary ion isotope
`saveDir` | Directory where the ptrSet object will be saved as .RData. If `NULL`, nothing will be saved.

### Value

a ptrSet object with slots :

- Parameter: list containing the parameters used for `createPrtSet`, `detectPeak` and `alignTimePeriods` functions.

- sampleMetadata: data frame containing information about the data, with file names in row names

- mzCalibRef: list containing for each file the masses used for the calibration (see `?ptairMS::calibration` for more details)

- signalCalibRef: mz and intensity +- 0.4Da around the calibration masses

- errorCalibPpm: list containing for each file the accuracy error in ppm at each calibration masses

- coefCalib: list containing the calibration coefficients 'a' and 'b' which enable to convert tof to mz for each file (see `calibration` function for more details.

- resolution: estimated resolution m / Δ m for each calibration masses within each file

- TIC: The Total Ion Current for each file

- timeLImit: list containing, for each file, a list of two element: the matrix of time limit for each file (if `fracMaxTIC` is different to zero), and the background index. See `timeLimits` for more details

- peakList: list containing for each file an expression set `eSet`, with m/z peak center, quantification for background and exhaled air in cps, ppb and ncps, and quantity for each time points. See `getPeakList` for more details.

### Examples

    library(ptairData)
    directory <- system.file('extdata/mycobacteria',  package = 'ptairData')
    ptrSet<-createPtrSet(dir=directory,setName='ptrSet'
    ,mzCalibRef=c(21.022,59.049),
    fracMaxTIC=0.9,saveDir= NULL)

[Package ptairMS version 1.0.1 Index]