peakCDFextraction {TargetSearch} | R Documentation

## NetCDF to R

### Description

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

### Usage

    peakCDFextraction(cdfFile, massRange)

### Arguments

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

### 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.

The `massRange` parameter used to be a numeric vector with two components: lower and higher masses. Now, the mass rangeis determined by scanning the CDF file. All masses in the CDF file will be extracted.

### Value

A two 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.

### Note

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

### Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

### See Also

`NetCDFPeakFinding`

[Package TargetSearch version 1.40.3 Index]