Metaboprep 1 pipeline

This function runs the original metaboprep1 pipeline using the old parameter file input format. The function requires access to the internet as the old package (default github commit `bbe1f85`) will be dynamically downloaded and used to process the data.

Usage

run_metaboprep1(parameter_file, gitcommit = "bbe1f85", attempt_report = FALSE)

Arguments

parameter_file

character, full file path to the metaboprep 1 parameter file

gitcommit

character, Github commit - default pinned to the last stable metaboprep 1 version `bbe1f85`

attempt_report

logical, whether to attempt metaboprep1 report generation. Default=FALSE as this can lead to errors on some operating systems.