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 1.38.2 Index]