Use PeakArea vs NormalizedPeakArea vs FGMS1Quantity for all Spectronaut datasets

[tonywu1999]

Story 1

MSstatsShiny gives no option to use either PeakArea (MS2) vs NormalizedPeakArea (MS2) vs FGMS1Quantity (MS1) for the intensity value. Users have preferences between the two, so we should enable that option.

For example, this dataset uses FG.MS1Quantity https://github.com/Vitek-Lab/MSstatsConvert/blob/devel/inst/tinytest/raw_data/Spectronaut/boxcar_protein_turnover_input.csv

Story 2

When uploading the chemoproteomics dataset under large file mode for spectronaut, we encounter this error:

Warning: Error in arrow::write_csv_arrow: x must be an object of class 'data.frame', 'RecordBatch', 'Dataset', 'Table', or 'RecordBatchReader' not 'arrow_dplyr_query'.

This occurs because we don't have the option to select the column name. In one of my datasets, F.NormalizedPeakArea is all NAs, which causes problems with arrow. We need users to be able to choose the column they select on Shiny for the intensity.

Subtasks

• Create a dropdown allowing users to pick between PeakArea vs NormalizedPeakArea vs FGMS1Quantity.
• Pass the user option into the loadpage server as the intensity parameter of the Spectronaut converter.
• Consider Refactor Loadpage UI & Server to Read First 100 Rows Upon Upload #160