e <
> lawrence.mich...@gene.com>, "bioc-devel@r-project.org" <
> bioc-devel@r-project.org>
> *Subject: *Re: [Bioc-devel] Compatibility of Bioconductor with tidyverse
> S3 classes/methods
>
>
>
> Thanks Guys for the discussion (I am learning a lot),
>
>
&g
Lawrence
, "bioc-devel@r-project.org"
Subject: Re: [Bioc-devel] Compatibility of Bioconductor with tidyverse S3
classes/methods
Thanks Guys for the discussion (I am learning a lot),
To Martin:
Thanks for the tips. I will start to implement those S4 style methods
https://
gt; an ‘internal’ function that implements the method on base R data types
>>>
>>> .foo <- function(x) {
>>> stopifnot("'x' must be a matrix" = is.matrix(x))
>>> t(x)
>>> }
>>>
>>> and m
t;> result <- .foo(x)
>> as_tibble(result)
>> })
>>
>> setMethod("foo", "SummarizedExperiment", function(x) {
>> result <- .foo(assay(x))
>> assays(x)[["foo"]] <- result
>>
uot;, function(x) {
> result <- .foo(assay(x))
> assays(x)[["foo"]] <- result
> x
> })
>
> One would expect the vignette and examples to primarily emphasize the use
> of the interoperable (SummmarizedExperiment) version.
>
> Ma
efano
Date: Friday, February 7, 2020 at 12:31 AM
To: Michael Lawrence
Cc: Martin Morgan , "bioc-devel@r-project.org"
Subject: Re: [Bioc-devel] Compatibility of Bioconductor with tidyverse S3
classes/methods
Would this scenario satisfy " make the package _directly_ compatible wit
Would this scenario satisfy " make the package _directly_ compatible with
standard Bioconductor data structures"
If an input is SummarizedExperiment return SummarizedExperiment, if the
input is a tbl_df or ttBulk, return ttBulk (?)
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fell
I would urge you to make the package _directly_ compatible with
standard Bioconductor data structures; no explicit conversion. But you
can create wrapper methods (even on an S3 generic) that perform the
conversion automatically. You'll probably want two separate APIs
though (in different styles), f
Thanks Michael,
yes in a sense, ttBulk and SummariseExperiment can be considere as two
interfaces. Would be fair enough to create a function that convert from one
to the other, although the default would be ttBulk?
*> I'm not sure the tidyverse is a great answer to the user interface,
because it
There's a difference between implementing software, where one wants
formal data structures, and providing a convenient user interface.
Software needs to interface with other software, so a package could
provide both types of interfaces, one based on rich (S4) data
structures, another on simpler str
Thanks a lot for your comment Martin and Michael,
Here I reply to Marti's comment. Michael I will try to implement your
solution!
I think a key point from
https://github.com/Bioconductor/Contributions/issues/1355#issuecomment-580977106
(that I was under-looking) is
*>> "So to sum up: if you subm
Martin's comments are great.
I'll just give some technical help. The "tbl_df" S4 class is already
defined by dplyr (and more properly), so omit the call to
setOldClass(). Then, things work a bit better.
> my %>% nest(-b) # had to fix this from your example
[some ugly result]
Warning messages:
1:
The idea isn't to use S4 at any cost, but to 'play well' with the Bioconductor
ecosystem, including writing robust and maintainable code.
This comment
https://github.com/Bioconductor/Contributions/issues/1355#issuecomment-580977106
provides some motivation; there was also an interesting exchang
Hello,
I have a package (ttBulk) under review. I have been told to replace the S3
system to S4. My package is based on the class tbl_df and must be fully
compatible with tidyverse methods (inheritance). After some tests and
research I understood that tidyverse ecosystem is not compatible with S4
c
14 matches
Mail list logo
