[Bioc-devel] FW: Repetitive variables within multiple function

[Vincent Carey]

in cbaf/R you could have a file cbaf-constants.R (this name is consistent
with the other filenaming in that folder) that includes assignments like the
one I sketched.  Your functions can then use the values defined in this
R program.

Your code would benefit from simplifications of this type ...  but all we
are
doing is avoiding redefinition of L1.characteristics in activities like

cbaf-obtainMultipleStudies.R:        existing.L1.charac <-
AvailableDataTypes[,2] %in% L1.characteristics

cbaf-obtainMultipleStudies.R:        f.condition <-
(AvailableDataTypes[,2])[existing.L1.charac]


There are opportunities for simplifying and improving trustworthiness

of code like that above that go beyond reducing the repetitive definition

of vectors of constants.  We can take it off list if you would like to

discuss further.




On Tue, Dec 31, 2019 at 10:27 AM Arman Shahrisa <shahrisa.arman using hotmail.com>
wrote:

> Thank you very much for your response. I really appreciate it.
>
>
>
> How can I define those vectors in my package? Another R script that
> possesses only
>
> all the vectors? Which also needs documentation. Am I correct?
>
>
>
> Best regards,
>
> Arman
>
>
>
> *From: *Vincent Carey <stvjc using channing.harvard.edu>
> *Sent: *‏سه شنبه,‏ ‏10 ‏دی ‏1398 ‏07:31
> *To: *Arman Shahrisa <shahrisa.arman using hotmail.com>
> *Cc: *bioc-devel <bioc-devel using r-project.org>
> *Subject: *Re: [Bioc-devel] Repetitive variables within multiple function
>
>
>
>
>
>
>
> On Mon, Dec 30, 2019 at 9:35 PM Arman Shahrisa <shahrisa.arman using hotmail.com>
> wrote:
>
> Hi to all,
>
> I’m the maintainer of the package cbaf. The package relies on various
> terms to find
> the cancer studies that possess specific data e.g. RNA-Seq.
>
> These terms are used by three various functions. I was wondering maybe it
> would be
> much better to include them in a separate file such as zzz.R so that every
> function
> could read the same variables. I already use the zzz.R file to print a
> message upon
> package loading on console.
>
> What is the best way to achieve what I’m looking for? I really appreciate
> any suggestions.
>
>
>
> I don't really understand the question.  I see some repetitiveness in
> grepping for "Tumor"
>
> in cbaf/R/*
>
>
>
> cbaf-availableData.R:      "Tumor Samples with mRNA data (RNA Seq V2)",
>
> cbaf-availableData.R:      "Tumors with mRNA data (RNA Seq V2)",
>
> cbaf-availableData.R:      "Tumor Samples with mRNA data (RNA Seq)",
>
> cbaf-availableData.R:      "Tumors with mRNA data (RNA Seq)",
>
> cbaf-availableData.R:    microRNA.Seq_terms_L1 <- c("Tumors with microRNA
> data (microRNA-Seq)",
>
> cbaf-availableData.R:                               "Tumor Samples with
> microRNA data (microRNA-Seq)"
>
> ...
>
> cbaf-obtainMultipleStudies.R:          c("Tumor Samples with mRNA data
> (RNA Seq V2)",
>
> cbaf-obtainMultipleStudies.R:            "Tumors with mRNA data (RNA Seq
> V2)",
>
> cbaf-obtainMultipleStudies.R:            "Tumor Samples with mRNA data
> (RNA Seq)",
>
> cbaf-obtainMultipleStudies.R:            "Tumors with mRNA data (RNA
> Seq)",
>
>
>
> Is your question about how to avoid repetitive definition of string
> constants in multiple
>
> functions?  There is no need to use zzz.R ... you can define your vectors
> of constants
>
> outside of functions in R code in your package.  The following is found
> inside one of your
>
> functions, and can't be seen by other functions that need the same content.
>
>
>
>   RNA.Seq_terms_L1 <- c("Tumor Samples with mRNA data (RNA Seq V2)",
>
>       "Tumors with mRNA data (RNA Seq V2)", "Samples with mRNA data (RNA
> Seq V2)",
>
>       "Tumor Samples with mRNA data (RNA Seq)", "Tumors with mRNA data
> (RNA Seq)",
>
>       "Samples with mRNA data (RNA Seq)")
>
>
>
>    But as long as this is defined outside of a function it will be
> accessible
>
> to any function in your package.  It can be documented and exported like
>
> any other value or function, should this be desired.  If not exported it
> will
>
> be private to code in the package.
>
>
> Best regards,
> Arman
>
>
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>
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