When re-processing already existing files, loading the MGF data (ie. reporter intensities) and the identification data into R takes quite some time in larger experiments.
Therefore, the loaded RAW intensities + the identification data could be cached in an RDS file and simply re-loaded when executing the R code.
If the search is re-triggered by the user (which would render the cached object invalid), the search routine automatically deletes the cached file anyways.
When re-processing already existing files, loading the MGF data (ie. reporter intensities) and the identification data into R takes quite some time in larger experiments.
Therefore, the loaded RAW intensities + the identification data could be cached in an RDS file and simply re-loaded when executing the R code.
If the search is re-triggered by the user (which would render the cached object invalid), the search routine automatically deletes the cached file anyways.