TargetSearchGUI {TargetSearch} | R Documentation

## A GUI for TargetSearch

### Description

Opens a Graphical User Interface (GUI, written using Tcl/Tk) to allow easy setting and manipulation of most processing parameters which control GC-MS Data Evaluation with TargetSearch.

NOTE: This function has been deprecated. Use the command line instead.

### Usage

        TargetSearchGUI()

### Details

The GUI is intended to facilitate the use of TargetSearch for users unfamiliar with R otherwise. Many parameters that would be set calling the individual TargetSearch Functions as described in the manual can be set here 'in one go' before running the complete analysis.

Important Note: Please select the folder where you store your GC-MS Data (NetCDF or Apex) as the `Working Directory`. It is not yet possible to process data files from other/different locations.

The parameters:

- `Working Directory`: Use the Browse-button to select the folder on your hard drive containing all your GC-MS data files. The output of TargetSearch will be written to this folder too.

- `File Import`: Clicking NetCDF Data or Apex Data radio buttons will open a file select dialog. Choose the files you would like to be processed. You may check your selection pressing the Show-button.

- `Baseline Correction`: Clicking on/off button will perform baseline correction before peak detection. If selected, the `threshold` parameter is a numeric value between 0 and 1. A value of one returns a baseline above the noise, 0.5 in the middle of the noise and 0 below the noise. See `baselineCorrection` for further details.

- `Retention Index Correction`: Retention Index Correction is neccessary and applied only if you supply NetCDF Data (Apex Data contain already Retention Indices). You may Load or Create the search windows for your RI-Markers here.

- `Peak Detection`: Search Windows refers to the allowed RI deviation of your metabolites which are narrowed in 3 consecutive searches. Intensity Counts threshold defines the minimum apex intensity incorporated in the analysis. A value of 1 would include all peaks. Mass Range allows to limit the mass values (m/z) to be included in the analysis. Smoothing averages raw data to eliminate some inherent noise leading to multiple peaks otherwise.

- `Library`: A Library (to detect metabolites) usable by TargetSearch contains at least information about the metabolite 'Name', its expected 'RI' and the selective masses in its spectrum 'SEL_MASS'. You may Load or Create one yourself using the respective buttons. The parameter no. of top masses is the number of most intensive masses that will be taken from the spectrum, and excluded masses is a list of masses that will be excluded. A more detailed description of the file formats can be found in `ImportLibrary`.

- `Normalization`: This selects how the data will be normalized during the metabolite search. Options are `"dayNorm"`, a day based median normalization, `"medianNorm"`, normalization using the median of all the intensities of a given mass, and `"none"`, no normalization at all.

- `Final Profiles`: Here you may set the parameters used by the functions `Profile` and `ProfileCleanUp`. timesplit sets an RI window that will be used to look for metabolites that could have been redundanly identified. correl. thr. is the correlation threshold and min. number of correlation samples is a threshold used to make sure that correlations are computed with at least said number of observations.

- `Parameters`: You may Save the current parameters as an `*.RData` file or Load previously saved parameters to compare the outcome of different settings or just repeat the analysis.

- `Program`: Run starts to process all currently selected files using the current parameters and saving output to Working Directory. Quit closes the GUI.

### Author(s)

Alvaro Cuadros, Jan Lisec

[Package TargetSearch version 1.40.3 Index]