Quiet parameter for keep_variable() about tidybulk HOT 8 CLOSED

Sure. I'll check and write the results here.

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Hello,

this message comes from edgeR (edgeR::filterByExpr), I would suggest to write to the maintainers.

All our messages are correctly wrapped under message() for this exact reason :)

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@stemangiola or could it be coming from this line in tidybulk https://github.com/stemangiola/tidybulk/blob/master/R/functions.R#L2568

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@stemangiola or could it be coming from this line in tidybulk https://github.com/stemangiola/tidybulk/blob/master/R/functions.R#L2568

Interesting! I have to double check although in that message there is no ## and is wrapped with the message() function which should respect the suppression.

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The keep_variable() function prints out the following phrase by default:
## Getting the 500 most variable genes

While it is not important for scripting, the message stays at the R markdown document even I designate knitr::opts_chunk$set(message = F)

Is it possible to suppress this message?

@canholyavkin do you feel like trying to comment the line https://github.com/stemangiola/tidybulk/blob/master/R/functions.R#L2568 and see if that issue goes away?

The issue is that the message() function should allow for silencing with global parameters. I am a bit puzzled.

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I commented the line at https://github.com/stemangiola/tidybulk/blob/master/R/functions.R#L2568.

When I set knitr::opts_chunk$set(message = F) or knitr::opts_chunk$set(message = T) the message of ## Getting the 500 most variable genes is gone now.

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I commented the line at https://github.com/stemangiola/tidybulk/blob/master/R/functions.R#L2568.

When I set knitr::opts_chunk$set(message = F) or knitr::opts_chunk$set(message = T) the message of ## Getting the 500 most variable genes is gone now.

Alright, @mblue9 is right as usual. XD

Thanks for doing it. The standard way to suppress messages is to wrap a command in suppressMessages(). That should work. I am not sure why knitr does not gives the same result.

Our approach is correct (using message() to print messages), unless I am missing something big.

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Thank you. :) suppressMessages() is worked. Have I nice day.

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