peakCDFextraction {TargetSearch} | R Documentation

## NetCDF to R

### Description

This function reads a netcdf chromatogram (format 3 or 4) file and returns a list containing raw data (retention time, intensity matrix) for easy manipulation.

### Usage

    peakCDFextraction(cdfFile, massRange)

### Arguments

`cdfFile` | A character string naming a netcdf file.
`massRange` | Deprecated. The mass range is extracted automatically.

### Details

The `cdfFile` is a path to a CDF-3 or a CDF-4 format file. The CDF-4 format file is a custom file used on `TargetSearch`.

The `massRange` parameter is deprecated but kept for compatibility. The actual m/z range is detected automatically and returned to the user.

### Value

A list with the following components:

`Time` | The retention time vector.
`Index` | The retention time index vector or NULL if unavailable.
`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.
`baselineCorrected` | Logical. It is `TRUE` if the file was baseline corrected by the function `baseline`. See note below.

### Note

This function does not look for peaks, just extracts all the raw intensity values of the chromatogram file. Use `NetCDFPeakFinding` instead.

The function does not know whether a CDF file was baseline corrected (for example by the GC-MS software vendor), unless it was performed by the function `baseline`. It is perfectably possible to have a baseline corrected file and the element `baselineCorrected` be `FALSE`.

### Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

### See Also

`NetCDFPeakFinding`, `baseline`.

[Package TargetSearch version 1.50.1 Index]