Update emd per matching sample metric #16
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give out max instead of everything
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Are you still working on this PR? |
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Yes I am. I have to change some stuff in it so it works with the new file schema. I'll change it from draft once it is ready.
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rcannood
approved these changes
Feb 13, 2025
src/metrics/emd/config.vsh.yaml
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| # test_setup: | ||
| # starter_file: | ||
| # samples_to_compare: | ||
| # - Tube1_Batch1_WT | ||
| # - Tube1_Batch2_WT |
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This can be removed
Suggested change
| # test_setup: | |
| # starter_file: | |
| # samples_to_compare: | |
| # - Tube1_Batch1_WT | |
| # - Tube1_Batch2_WT |
src/metrics/emd/config.vsh.yaml
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| # Keep for now for future metrics' reference if required | ||
| # arguments: | ||
| # - name: "--samples_to_compare" | ||
| # type: "string" | ||
| # description: 2 samples to compare. | ||
| # required: true | ||
| # multiple: true | ||
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Remove if you don't need it ;)
Suggested change
| # Keep for now for future metrics' reference if required | |
| # arguments: | |
| # - name: "--samples_to_compare" | |
| # type: "string" | |
| # description: 2 samples to compare. | |
| # required: true | |
| # multiple: true |
removed unnecessary flags
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Describe your changes
Update EMD per sample metric so it doesn't need the sample flag and the layer flag.
The samples to calculate the metric is automatically inferred from the input_integrated and input_validation datasets.
Input_validation is needed because for some donors, the matching samples may not be given to the batch correction algorithm but is required to compute the metric.
Layer from each dataset is set to "integrated" and "preprocessed" automatically. This is ok as these layers are specified in respective files' yaml.
Checklist before requesting a review
I have performed a self-review of my code
Check the correct box. Does this PR contain:
Proposed changes are described in the CHANGELOG.md
CI Tests succeed and look good!