CompToxFullCSVtoLocalCSVterms: Prepare CompTox Dashboard Full CSV file for MetFragCL
In schymane/ReSOLUTION: SOLUTIONS for High ReSOLUTION Mass Spectrometry

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

This function extracts metadata headers from the CompTox CSV download file for use in MetFragCL. It reads metadata field names for inclusion as scoring terms.

1	CompToxFullCSVtoLocalCSVterms(csv_file, start_index=13, TermsToRemove="default")

`csv_file`	Full path and file name to the Dashboard CSV Download file to process
`start_index`	The column number where the metadata columns start (default `13` is appropriate for CompTox Dashboard Download file designed specifically for MetFrag)
`TermsToRemove`	Define column headers to remove from scoring terms. Select default values using `"default"` (see details) or add a vector of strings. `c()`

The current default TermsToRemove are c("TOXCAST_NUMBER_OF_ASSAYS/TOTAL","TOXVAL_Link", "PPRTV_Link", "IRIS_Link"). This option removes the terms from MetFrag scoring to avoid processing errors, but these columns are retained in the results file, for downstream use if desired. If MetFrag exits with a status=5, check the log file for terms to add to this list.

Returns a list containing the CSV file name, a list of scoring terms to add to the MetFrag config file and a corresponding score weights entry.

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

MetFragConfig, runMetFrag

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# note this is an example off a limited file
CompToxFullCSVFile <- system.file("extdata","dsstox_MS_Ready_MetFragTestCSV5.csv",package="ReSOLUTION")
LocalCSVterms <- CompToxCSVtoLocalCSVterms(CompToxFullCSVFile)