NetCDFPeakFinding {TargetSearch} | R Documentation

## Peak picking algorithm from CDF files

### Description

This function reads a netcdf chromatogram file, finds the apex intensities and returns a list containing the retention time and the intensity matrices.

### Usage

    NetCDFPeakFinding(cdfFile, massRange = NULL, Window = 15, IntThreshold = 10,
                      pp.method = "ppc", baseline = FALSE, baseline.opts = NULL)

### Arguments

`cdfFile` | A character string naming a netcdf file.
`massRange` | Deprecated. It is completely ignored but it is kept for compatibility with old scripts.
`Window` | The window used by peak picking method. The number of points actually used is `2*Window + 1`.
`IntThreshold` | Apex intensities lower than this value will be removed from the RI files.
`pp.method` | The pick picking method to be used. Options are `"smoothing"`, `"gaussian"` and `"ppc"`.
`baseline` | Logical. Should baseline correction be performed?
`baseline.opts` | A list of options passed to `baselineCorrection`

.

### Details

The function expects the following NetCDF variables: `intensity_values`, `mass_values`, `scan_index`, `point_count` and `scan_acquisition_time`. Otherwise, an error will be displayed.

Formerly, the `massRange` parameter was a numeric vector with two components: lower and higher masses. Now, the mass range is detected automatically and it has no effect if it is set. It is kept only for compatibility reasons.

There are three peak picking algorithms that can be used. The `"smoothing"` method smooths the m/z curves by a moving average and then looks for a change of sign of the intensity difference between two consecutive points. The `"gaussian"` is exactly the same, but it uses a gaussian smoother instead of a moving average.

The `"ppc"` uses a sliding window and looks for the local maxima. This method is based on R-package `ppc`.

### Value

A three component list.

`Time` | The retention time vector.
`Peaks` | The intensity matrix. Rows are the retention times and columns are masses. The first column is the lower mass value and the last one is the higher mass.
`massRange` | The mass range.

### Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

### See Also

`peakCDFextraction`

### Examples

    require(TargetSearchData)
    CDFpath <- file.path(find.package("TargetSearchData"), "gc-ms-data")
    CDFfiles <- dir(CDFpath, pattern = ".cdf$", full.names = TRUE)
    CDFfiles

    # extrac peaks of first chromatogram
    peaks.1 <- NetCDFPeakFinding(CDFfiles[1], Window = 15, IntThreshold = 10, pp.method = "smoothing")
    # scan acquisition times
    head(peaks.1$Time)
    # peaks in matrix form. first column is mass 85, last one is mass 320.
    head(peaks.1$Peaks)

[Package TargetSearch version 1.40.3 Index]