`verbose` argument for `transformAssay` (`.apply_pseudocount`) (and maybe other functions?)

[nr0cinu]

Is your feature request related to a problem? Please describe.

I'd would like to easily control the level of output from mia, because I am using it in targetsworkflows and extra output is not useful or even counterproductive.

Describe the solution you'd like

Add a boolean verbose argument to transformAssay that turns of all messages and warnings. Default should be TRUE, so that I can turn it off when needed in longer workflows.

Describe alternatives you've considered

suppressMessages/Warnings or purrr's quietly would work, but it does not work well when using longer statements with pipes (|>) and is imho clunkier than a simple verbose argument.

Thanks!

PS: I can also provide a pull request for this if preferred :)

[TuomasBorman]

Hi @nr0cinu! Sorry for late reply.

The reason of using message/warning is that they can be suppressed. However, there are some limitations as you pointed out.

One option could be to create new function

msg <- function(msg, .call = TRUE, verbose = TRUE, ...){
    if(verbose){
        message(msg, call. = call.)
    }
}

Then message could be just replaced with msg (and warning with wrn)

Then this does not cause too many changes in files.

PR would be nice!

-Tuomas

[nr0cinu]

Thanks for the feedback. I will draft a PR for this :)

[antagomir]

@nr0cinu any updates?

[nr0cinu]

I did not manage to work on this yet. I still plan to tho :)

[antagomir]

That would be great. Also cool if we can try to get this done & completed :-)

[nr0cinu]

Feel free to implement yourself :) I'll comment once I start working on it, so there is no double work :)