README.md

# superShiny 2024

## Input

Excel file with the following sheets

- `SAMPLE`
- `MEASUREMENT`
- `FEATURE` (optional, because of old format)

`FEATURE` currently not supported

## Parsing

1. Feature names are split. Internal standards are identified and base compounds name extracted
2. Measurement data frame is prepared for normalisation. Internal standards, biological normalisation, TIC and associated standard all possible

## Work steps

1. `Input` from server or old school. Server part rewritten.
2. `Standard`: display all available normalisation variables
3. `PCA`: normalise and display PCA

- pca figure size to global preferences
- my_proc$res created already by parse
- check 'baseline'
- check correlation check
- create input file with pools
- create input file mz/rt
- compound db with plot order

## Newest

- Keep pool samples
- Pool samples may have missing values in experimental design columns
- Pool samples may have missing values in normalisation columns (replaced by mean)

## Bug

- when last outlist item is removed, my_proc$outlist == NULL, does not update

## yeti

- Overhauled Infile tab error messages
- Load custom comp_db
- Overhauled Stan tab plot appearance options