Restructuring of R code into a more condensed format
Passing variables from python to R via option arguments.
Current Behavior
There are separate R files (ex: "run_dada_single.R") dedicated to processing each tech-specific read type with the exception of pyro sequencing which utilizes the same script as single-end reads.
Arguments are passed from the python script "_denoise.py" to the supporting R scripts through positional arguments.
Proposed Behavior
With the large amount of redundant code between the various supporting R files I think it makes sense to condense these into one or two R files to more easily enable code to be shared between the various tech-specific data processing functionalities.
Changing the method of argument passing from positional to optional (utilizing variable names); I believe, would make it easier to expand functionality further down the line as well as make it more explicit as to which variables are being passed and how they are being used.
Comments
Hi All! I just wanted to mention that I am working with @benjjneb as a grad student to look into implementing the changes described above.
Improvement Description
Current Behavior
Proposed Behavior
Comments