Jonathan CarrollAug 11, 2024

A bigger post than usual this time, but I wanted to cover as much of the background as I could...

https://jcarroll.com.au/2024/08/11/tidy-dataframes-but-not-tibbles/

{DFplyr} - use {dplyr} functions on an S4Vectors::DataFrame

#rstats #bioconductor #tidyomics

Tidy DataFrames but not Tibbles

A while ago (2019 seems so long ago now) I started working on something I thought was interesting but which never really got any traction. It has potential once more, so it’s about time I wrote up what it does and why I think it’s a useful idea. I’m going to talk about using the {dplyr} package on some data with rows and columns, but we’re not talking about data.frames or tibbles…

Irregularly Scheduled Programming
Show threadDr. Robert M FlightAug 11, 2024

@jonocarroll As I was reading through the post, I'm thinking to myself that this *sounds* a lot like some of the functionality available in {tidyomics} for subsetting assay data based on metadata using tidyish principles.

And then you link to {tidyomics} at the end. 🤦‍♂️

I think it definitely looks like it would be worth getting in touch with @mikelove about seeing how it might better fit in {tidyomics}.

Also, wrong link to tidyomics. I think this should be https://github.com/tidyomics

tidyomics

Open project to create tidy analysis packages for omics data - tidyomics

GitHub
Show threadJonathan CarrollAug 11, 2024
@rmflight @mikelove this post is actually a pre-read for a talk I'm giving to the tidyomics group this week. It turns out Stefano and I live in the same city.
Show threadDr. Robert M Flight

@jonocarroll @mikelove ah, that makes sense.

Looks like a really nice idea Jonathan. I've been using summarizedExperiment objects more and more often in my analyses, and that `|> as.data.frame() or as_tibble()` definitely gets annoying, especially as you mention, now it's not part of the dataset anymore.

Aug 11, 2024 at 10:00pmMegalodon
Show threadJonathan CarrollAug 11, 2024
@rmflight @mikelove I'm definitely keen to hear what isn't working or is missing from {DFplyr} from people who actually do analyses. I mainly just chop up SEs with some filters.
Show threadMichael LoveAug 13, 2024

@rmflight @jonocarroll

excited to hear about it tonight. By the way, these calls and the Slack channel are totally open, you can find us via #tidiness_in_bioc on Bioc slack