Fix FDR formula #1477
Open
Fix FDR formula #1477
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Based on the current formulation of the FDR, datasets having high decoy scores can lead to FDR values > 1 leading to loss of some annotations when preparing results by applying a cutoff of FDR < 1 (https://github.com/metaspace2020/metaspace/blob/6661211be8c87c2ff617f2cb8716a128bdc3915d/metaspace/engine/sm/engine/annotation_lithops/prepare_results.py#L74). This fixes the FDR calculation by adding the weighted decoy term to the denominator as well to make sure that FDR is always [0-1].
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Based on the current formulation of the FDR, datasets having high decoy scores can lead to FDR values > 1 leading to loss of some annotations when preparing results by applying a cutoff of FDR < 1 (
metaspace/metaspace/engine/sm/engine/annotation_lithops/prepare_results.py
Line 74 in 6661211
This fixes the FDR calculation by adding the weighted decoy term to the denominator as well to make sure that FDR is always [0-1].