(Just sharing my thoughts as those days I am spending quite
some time preparing the upgrade of a Bioconductor package).
Le Fri, Oct 20, 2017 at 12:50:48AM +0000, Ryan Thompson a écrit :
>
> gene_client <- BioThingsClient("gene")
> query("CDK2", client=gene_client)
In addition, since the piping operator (%>%) of dplyr and magrittr is
gaining traction, I would recommend to carefully consider which will be
the first argument of the function:
With the client as first argument, one can then write things like:
gene_client %>% query("CDK2") # similar to query(gene_client, "CDK2")
With the gene symbol as first argument:
"CDK2" %>% query(gene_client) # similar to query("CDK2", gene_client)
If gene symbols may come as output from other commands and the query
function is able to work smartly with a vector of gene symbols as input,
then the second pattern might be useful. Otherwise the first pattern
probably makes more sense.
See https://cran.r-project.org/web/packages/magrittr/vignettes/magrittr.html
for details.
(Note however that the piped and non-piped functions are not exactly
equivalent, and that piped commands can be harder to debug; therefore
it may be better to only use them in interactive sessions.)
Have a nice day,
--
Charles Plessy
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