Description Usage Arguments Value Author(s) References
This is a wrapper function for GenForm, requiring MS, MS/MS, ion settings and directories.
1 2 3 |
ms_file |
File name of a plain text, two column file (e.g. |
msms_file |
A plain text, two column file (e.g. |
ion |
Ion setting to use. Options: |
GenFormDir |
Directory containing |
ResultsDir |
Directory to save the GenForm results. Existing files will be overwritten. |
ppm |
Accuracy setting for MS1 (default |
acc |
Accuracy setting for MS2 (default |
elements |
Selection of elements to consider. Default |
ff |
A "fuzzy formula" input to offer more control beyond |
dbe |
Default |
oei |
Default |
mz |
If mz is >0, this is the mass GenForm will use to calculate the formulas, considering
the |
exist |
Default |
an_loss |
Activate the annotation of MSMS fragments with subformulas and losses. |
an_loss_limit |
Define the cut-off limit for annotating subformulas and losses. For many peaks and formulas, this becomes time consuming and produces massive files of limited use. |
sort |
Default |
cleanMSMS |
Default |
Several files containing various GenForm outputs.
Emma Schymanski (R wrapper, emma.schymanski@uni.lu
) and Markus Meringer (GenForm)
GenForm on Source Forge: https://sourceforge.net/projects/genform/
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