Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

fix asterisks in gene names #199

Merged
merged 2 commits into from
Dec 14, 2023
Merged

fix asterisks in gene names #199

merged 2 commits into from
Dec 14, 2023

Conversation

GWMcElfresh
Copy link
Contributor

This is a small bugfix toFitRegularizedClassificationGlm() to allow specifically gene UGT2B9*2 (the asterisk being the problem) to pass through MLR3's pipelines.

@bbimber
Copy link
Contributor

bbimber commented Dec 14, 2023

@GWMcElfresh: just one comment. You are doing things like this:

gsub("\\*", "star", colnames(target_labeled_data))

this would break if a gene happened to contain the string star, right? same for dash, etc. Could we do anything to make the replacement strings more likely to be unique? Can we use any other characters, such as:

star

-star-

or anything that would make these placeholder strings more likely to never occur in a real gene name?

@GWMcElfresh
Copy link
Contributor Author

@GWMcElfresh: just one comment. You are doing things like this:

gsub("\\*", "star", colnames(target_labeled_data))

this would break if a gene happened to contain the string star, right? same for dash, etc. Could we do anything to make the replacement strings more likely to be unique? Can we use any other characters, such as:

star ⭐ -star-

or anything that would make these placeholder strings more likely to never occur in a real gene name?

I checked out lower case letters in the mmul10 genome and the only lower case occurrences are ORF (e.g. "C15H9orf24", "C9orf72"), so I think we're safe here so far.

@GWMcElfresh GWMcElfresh merged commit 0065bcc into master Dec 14, 2023
3 checks passed
@GWMcElfresh GWMcElfresh deleted the fixGlmFeatureNames branch December 14, 2023 20:51
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants