Add alphaMissense in functional impact column #5042
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onursumer
approved these changes
Nov 14, 2024
| arrowEl.style.display = 'none'; | ||
| } | ||
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| export const AlphaMissense_URL: string = |
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Do we need an underscore here?
Suggested change
| export const AlphaMissense_URL: string = | |
| export const AlphaMissenseURL: string = |
| interface IFunctionalImpactColumnTooltipState { | ||
| active: 'mutationAssessor' | 'sift' | 'polyPhen2'; | ||
| } | ||
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| enum FunctionalImpactColumnsName { |
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Not a big deal but FunctionalImpactColumnName might be a better name
| legend() { | ||
| const showMutationAssessor = shouldShowMutationAssessor(); | ||
| // Each line in the legend table uses the same style (mutationAssessorStyles) |
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maybe rename mutationAssessorStyles to functionalImpactStyles or something like that?
| FunctionalImpactColumnTooltip.siftText()} | ||
| {this.state.active === 'polyPhen2' && | ||
| FunctionalImpactColumnTooltip.polyPhen2Text()} | ||
| {this.state.active === |
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Should we use mobx here instead of react state? I think we used to avoid built-in react state in favor of mobx. Not sure if we are still following that practice though.
inodb
approved these changes
Nov 14, 2024
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Add alphaMissense in functional impact column. There are three discrete categories: 'benign', 'pathogenic', or 'ambiguous'. These are derived using the following thresholds: 'benign' if alphamissense_pathogenicity < 0.34; 'pathogenic' if alphamissense_pathogenicity > 0.564; and 'ambiguous' otherwise (category assignments are based on their website)
Test:
link
Add
Functional Impactcolumn:Hover over AlphaMissense dots, tooltip shows more information:
Download: