CompToxXLStoLocalCSVterms: Prepare CompTox Dashboard MetFrag Export XLS files for...

In schymane/ReSOLUTION: SOLUTIONS for High ReSOLUTION Mass Spectrometry

Description

This function prepares CompTox XLS Export files for use in MetFragCL. It converts the XLS to a CSV and extracts numeric metadata field names for inclusion as scoring terms.

Usage

CompToxXLStoLocalCSVterms(xls_file, start_index=15, csv_file= "")

Arguments

xls_file	Full path and file name to the Dashboard Export file to process
start_index	The column number where the metadata columns start (default 15 is appropriate for CompTox Dashboard MetFragBeta Export file format released March 2018)
csv_file	If empty, the CSV file will have the same name as xls_file except the file ending. Enter a file name here if you wish to have a different named file. If a CSV file with the same name exists in the directory it is overwritten.

Value

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.

Author(s)

Emma Schymanski <[e-mail]> in partnership with Christoph Ruttkies (MetFragCL), Antony J. Williams and team (CompTox Dashboard)

See Also

MetFragConfig, runMetFrag

Examples

CompToxXLS <- system.file("extdata","CompToxBatchSearch_MetFrag_MSready_C10H14N2.xls",package="ReSOLUTION")
LocalCSVterms <- CompToxXLStoLocalCSVterms(CompToxXLS)

schymane/ReSOLUTION documentation built on May 22, 2021, 3:41 a.m.