Improve the way of reading input matrix files in R templates
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Description
Is your feature request related to a problem? Please describe
Currently, propr/logratio and propr/propd read the matrix input, fix either gene_id or gene_name as row index, then remove the other one in a hard-coded way. Sometimes, those columns are named differently.
Describe the solution you'd like
The user should provide the gene_id_col and gene_name_col as ext.args and then keep the one that is interested, and remove the other one .
Describe alternatives you've considered
No response
Additional context
modules:
- propr/logratio
- propr/propd
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the propr/logratio and propr/propd module templates and reading how each currently parses matrix input and handles ext.args. Done means both modules let users provide gene_id_col and gene_name_col, retain the requested column, and remove the other without relying on fixed column names.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100