Automatic creation of targets.csv file

[tjthurman]

Currently, I'm keeping the behavior of the make_targets() function, which automatically saves a targets.csv file in the current working directory. That file contains the targets, as imported. This is maybe not ideal, from a function design perspective. Its sort of a "side-effect" of the main goal of the make_targets() function (which is to import data, not to write it), and there's no customization.

So, first question: Do we need this targets.csv file at all? If so, should we split off the saving into its own function (e.g., write_target_file()) to remove the side effect, and maybe to allow some more customization of directory and/or filename? Honestly, we don't even really need a custom function: just write.csv() would work.

[ByrumLab]

I didn't know where the targets.csv file was coming from. I don't need it.

[clw09]

I agree it is definitely not the best design to generate a generic targets.csv as a byproduct. I auto generated the file for testing purposes to make sure things were matching up. :) Until we can sort out streamlining the metadata and data import portion, I think we should probably save a copy of the metadata that is generated since it contains the matched sampleIDs from the sample report for all samples, which are not included in the metadata file that is imported. Maybe a copy for out records and one in the protein_analysis folder for the PI. What do you guys think?

Cheers!

Charity L. Washam, PhD

Instructor of Biochemistry and Molecular Biology

Bioinformatician, UAMS Bioinformatics Core

University of Arkansas for Medical Sciences

4301 W Markham St., Slot 516

Little Rock, Arkansas 72205

Bioinformatician, CTPR Genomics and Bioinformatics Resource

Center for Translational Pediatric Research (CTPR)

(www.archildrens.org/archildrens-COBRE)

Arkansas Children's Research Institute (ACRI)

13 Children’s Way, Slot 512-47

Little Rock, Arkansas 72202-3591

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From: ByrumLab @.> Sent: Wednesday, September 14, 2022 11:12:21 AM To: ByrumLab/proteomicsDIA @.> Cc: Subscribed @.***> Subject: Re: [ByrumLab/proteomicsDIA] Automatic creation of targets.csv file (Issue #79)

I didn't know where the targets.csv file was coming from. I don't need it.

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[ByrumLab]

No copy to the PI in protein_analysis. This is internal check only. I wouldn't even write it as a default but can use write_csv if need to check something.

[tjthurman]

OK, I'm removing the target.csv creation and have added in the README example pipeline a note that you can save the .csv if you want.