Message-ID: <173e380d-a408-6434-a7f9-26cc7646ed19@fgcz.ethz.ch>
Date: 2021-11-18T17:00:11Z
From: Witold E Wolski
Subject: [Bioc-devel] EXTERNAL: LazyData: false and accessing data in the YAML section of an Rmd document
In-Reply-To: <a2703f44-9be1-5210-709f-8f70d6f7a3a2@roswellpark.org>
I guess I failed to explain:
In the yaml section of the rmarkdown I can only use a single R expression;
i.e., I can not write:
```
configuration: !r data('somedata', package="xyz"); somedata$uvw
```
because these are two expressions.
I could write:
xyz::somedata$uvw
So to rephrase my question. What would be your recommendation to convert
these two expressions:
data('somedata', package="xyz"); somedata$uvw
into one?
Hope this clarifies my question.
Best regards
Witek
On 18/11/2021 16:44, Marcel Ramos wrote:
> Hi Witold,
>
> I am not sure what the use case is for loading data in the yaml header.
> If you're swapping out data for your vignettes, perhaps your introduction
> chunks could contain the code to load the data.
>
> In any case, I recommend that you use `data("dataset", package = "package")`
> to load the data with LazyData turned off.
>
> Best regards,
>
> Marcel
>
> On 11/18/21 9:51 AM, Witold Wolski wrote:
>> Hi,
>>
>> I with BiocCheck I am getting a warning that my packages uses
>> LazyData: true.
>>
>> So far some of the package vignettes loaded the data in the params
>> section of the Rmd file e.g.,
>>
>> ---
>> title:
>> ...
>> ...
>> params:
>> ? configuration:? !r data(prolfqua::data_ionstar);
>> quote(prolfqua::data_ionstar$filtered()$config )
>> ? project_conf: NULL
>> ? data: !r quote( prolfqua::data_ionstar$filtered()$data )
>> ...
>> ---
>>
>>
>> However, this will not work with LazyData false. What is the
>> bioconductor way of loading the data in the Rmd file Yaml section?
>>
>> If anyone wonders, why do I need it. By this I can reuse the vignette
>> with a different dataset.
>>
>> Best Witold
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> ---
> Marcel Ramos
> Bioconductor Core Team
> Roswell Park Comprehensive Cancer Center
> Dept. of Biostatistics & Bioinformatics
> Elm St. & Carlton St.
> Buffalo, New York 14263
>
>
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>
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