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

Create unit tests for HTTR signature data fit with tcplfit2 #37

Open
3 tasks
sedavid01 opened this issue Sep 12, 2023 · 1 comment
Open
3 tasks

Create unit tests for HTTR signature data fit with tcplfit2 #37

sedavid01 opened this issue Sep 12, 2023 · 1 comment

Comments

@sedavid01
Copy link
Collaborator

Goal: The goal of this issue is to create unit tests for high-throughput transcriptomics (HTTR) signature data such that we ensure that as the codebase of tcplfit2 is updated that the updates do not break/alter the results previously obtained in previous analyses with tcplfit2.

Needs for finishing this ticket:

  • Choose a manageable subset of the overall data provided by the HTTR team - verify the chosen set covers many (if not all) scenarios of interest
  • Create an RData file for the package (may want to ensure we do NOT want this to be exported from the package)
  • Create a unit test ensuring that the results for HTTR remain consistent from version to version of tcplfit2
@sedavid01
Copy link
Collaborator Author

Baseline sampling strategy:

  • utilize the previous used criteria for HTPP to fulfill needs we need to meet
  • if there are any signature categories that can be identified then do random selections in a stratified manner - Grace mentioned there were GO and CMAP ( choose 10 genes per category, then 30 other randomly selected genes)
  • like with the genes - if a baseline of 50 signatures (covering the previous bullet) is relatively fast, then may look to bump up to 100 signatures (20 per category and 60 other random signatures).

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

When branches are created from issues, their pull requests are automatically linked.

1 participant