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

[Arman Shahrisa]

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<mailto:stvjc using channing.harvard.edu>
Sent: ‏سه شنبه,‏ ‏10 ‏دی ‏1398 ‏07:31
To: Arman Shahrisa<mailto:shahrisa.arman using hotmail.com>
Cc: bioc-devel<mailto: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<mailto: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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