feat(metamorpheus-converter): Add clean functionality of metamorpheus converter

[tonywu1999]

Description

As a part of this issue, users are requesting a converter from Metamorpheus to MSstatsPTM.

The first step is to create a converter from Metamorpheus to MSstats.

Changes

1. Set up implementation for MSstatsClean for Metamorpheus
   1. Features consist of peptide sequence + precursor charge given Metamorpheus handles DDA experiments.
2. Added annotation data from Metamorpheus into raw data folder
3. Added RDS file of MSstatsInputFiles object of Metamorpheus input data into a new processed_data folder for unit testing purposes
4. Adjusted documentation via devtools::document()

Testing

1. Verified that MSstatsClean works as expected for Metamorpheus input
2. Added unit tests verifying MSstatsClean works as expected for Metamorpheus input
3. Installed and ran RStudio check locally and everything succeeds.

Next Steps

1. Squash & Merge
2. Create MetamorpheusToMSstats function for core MSstats package
3. Create MetamorpheusToMSstatsPTM function for MSstatsPTM package

[devonjkohler]

Looks good! We can merge this in if Matt doesn't have any changes.

[mstaniak]

Why rds rather than a text file?

[tonywu1999]

@mstaniak

I used an RDS file for unit testing purposes.

The output of the MSstatsImport function is an MSstatsMetamorpheusFiles object, and I wanted to use that object as the input of MSstatsClean for unit tests. At the same time, I wanted to test MSstatsClean independently from other functions. As a result, I saved the object as an RDS file and read the RDS file as input for unit tests.

[tonywu1999]

To make things less confusing, I'll change the name of the RDS file to be something like "MSstatsMetamorpheusFilesObject.rds" to make it clear it's an object of class MSstatsMetamorpheusFiles and has nothing to do with the output of Metamorpheus directly.

[mstaniak]

Looks good, only question is about the rds format.

[mstaniak]

Lets's move this rds file from raw_data to processed_data (or a similar name) and we're good to go