TargetSearchGUI: 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.
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.