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Add help popup for SCHEMA gene results
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nawatts committed Sep 11, 2020
1 parent 749e5d3 commit 91a3ced
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14 changes: 13 additions & 1 deletion src/browsers/schema/SCHEMAGeneResults.js
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Expand Up @@ -4,6 +4,10 @@ import styled from 'styled-components'

import { BaseTable, TooltipAnchor, TooltipHint } from '@gnomad/ui'

import HelpButton from '../base/HelpButton'
import StyledContent from '../base/StyledContent'
import geneResultsDescription from './content/generesults.md'

const Table = styled(BaseTable)`
min-width: 325px;
`
Expand Down Expand Up @@ -160,7 +164,15 @@ SCHEMAGeneResult.propTypes = {

const SCHEMAGeneResults = ({ results }) => (
<>
<h2>Gene Result</h2>
<h2>
Gene Result{' '}
<HelpButton
popupTitle="Gene Result"
popupContent={
<StyledContent dangerouslySetInnerHTML={{ __html: geneResultsDescription.html }} />
}
/>
</h2>
{results.meta ? <SCHEMAGeneResult result={results.meta} /> : <p>No result for this gene.</p>}
</>
)
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4 changes: 1 addition & 3 deletions src/browsers/schema/content/generesults.md
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@@ -1,9 +1,7 @@
# Gene results description [question mark]

This table displays aggregated case-control and _de novo_ counts for the purposes of gene discovery. We first enriched for pathogenic variants by restricting our analysis to ultra-rare protein-coding variants (defined as minor allele count [MAC] ≤ 5) in our data set.

Given empirically observed exome-wide burden, we focused on protein-truncating or putatively loss-of-function variants (PTVs), defined as stop-gained, frameshift, and essential splice donor or acceptor variants. We additionally analyzed damaging missense variants as prioritized by the MPC pathogenicity score (see [Samocha _et al_. 2017](https://www.biorxiv.org/content/10.1101/148353v1)).

PTVs and MPC > 3 missense variants (defined as Class I variants) were jointly analyzed in a single case-control burden test. MPC 2 - 3 variants (defined as Class II variants) were analyzed in a separate burden test before meta-analyzed with the Class I burden P-value using Stouffer's weighted Z-score method. Case-control significance was evaluated using a permutation-based Fisher's Exact Test. For genes with case-control P-value < 0.01, _de novo_ Class I and II P values were calculated using the Poisson rate test and meta-analyzed with our case-control test statistic using a Stouffer's weighted Z-score method. The Q-value is the P-value adjusted for the False Discovery Rate.

For a full description and justification of the approach, please consider the main text and supplementary materials and methods of the SCHEMA pre-print manuscript.
For a full description and justification of the approach, please consider the main text and supplementary materials and methods of the SCHEMA pre-print manuscript.

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