MetFragConfig.formula: Create MetFrag Config Files with Molecular Formula Candidate...
In schymane/ReSOLUTION: SOLUTIONS for High ReSOLUTION Mass Spectrometry

Description Usage Arguments Details Value Author(s) See Also Examples

This is a molecular formula-specific wrapper function for MetFragConfig.

1	MetFragConfig.formula(mol_form, adduct_type, IsPosMode, results_filename, peaklist_path, base_dir, ...)

`mol_form`	The molecular formula (as a string) with which to search the candidate database (`DB`). `mass` is calculated automatically.
`adduct_type`	The adduct species used to define mass (if `neutralPrecursorMass=FALSE`) and fragmentation settings in the config file, entered as either `PrecursorIonType` (text) or `PrecursorIonmode` (a number). The available options are given in the system file `MetFragAdductTypes.csv` in the `extdata` folder. Recommended default values (if ion state is unclear) are `[M+H]+` (1) for positive and `[M-H]-` (-1) for negative mode.
`results_filename`	Enter a base filename for naming the results files - do not include file endings
`peaklist_path`	Enter the full path and file name to the peak list for this config file
`base_dir`	Enter the directory name to set up the subfolders for MetFrag batch results. If the folders don't exist, subfolders `config`, `log` and `results` are created; the output of this function is saved in `config`.
`isPosMode`	Use `TRUE` or `FALSE` to set positive or negative ionization as appropriate.

Remaining parameters are described in MetFragConfig

Returns a MetFrag config file name

Emma Schymanski <emma.schymanski@uni.lu> in partnership with Christoph Ruttkies (MetFragCL), Antony J. Williams and team (CompTox Dashboard)

MetFragConfig, runMetFrag, getAdductMassesFromFormula

# Example of Simazine
peaklist_path <- system.file("extdata","EA026206_Simazine_peaks.txt",package="ReSOLUTION")
# change this directory to an existing one, or this example won't work
test_dir <- "C:/DATA/Workflow/MetFrag22/metfrag_test_results"
testCSV <- system.file("extdata","dsstox_MS_Ready_MetFragTestCSV5.csv",package="ReSOLUTION")

config_file <- MetFragConfig.formula("C7H12ClN5","[M+H]+",IsPosMode=TRUE, "Simazine_formula_PubChem",peaklist_path, test_dir,
DB="PubChem")
config_file2 <- MetFragConfig.formula("C7H12ClN5",1,IsPosMode=TRUE, "Simazine_formula_CompTox",peaklist_path,test_dir,
DB="LocalCSV",localDB_path=testCSV)
config_file3 <- MetFragConfig.formula("C7H12ClN5",1,IsPosMode=TRUE, "Simazine_formula_CompTox_noInChIFilter",peaklist_path,test_dir,
DB="LocalCSV",localDB_path=testCSV,filter_by_InChIKey = FALSE)

metfrag_dir <- "C:/DATA/Workflow/MetFrag22/"
MetFragCL_name <- "MetFrag2.4.4-msready-CL.jar"
#note this first query is a longer query using PubChem
runMetFrag(config_file, metfrag_dir, MetFragCL_name)
runMetFrag(config_file2, metfrag_dir, MetFragCL_name)
runMetFrag(config_file3, metfrag_dir, MetFragCL_name)