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GDC support 5-category cnv #2545
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shared/utils/src/common.js
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@@ -282,6 +282,7 @@ mclass[mclasssv] = { | |||
key: mclasssv | |||
} | |||
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//TODO:CNV_amp should be repalced with CNV_gain to avoid confusion with CNV amplification (CNV_amplification) below |
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unfortunately "CNV_amp" may have to stay as-is since it may be hardcoded in lots of data beyond portal code.
can add a comment to clarify above, also CNV_amp really means "CNV Gain", which is used in both 2-category and 5-category CNV data representation
@@ -300,6 +301,24 @@ mclass[mclasscnvloss] = { | |||
key: mclasscnvloss | |||
} | |||
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export const mclasscnvAmp = 'CNV_amplification' |
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please make a note this is next level above mclasscnvgain
and is used in 5-category CNV data
client/plots/matrix/matrix.cells.js
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@@ -223,7 +223,18 @@ export function setGeneVariantCellProps(cell, tw, anno, value, s, t, self, width | |||
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// return the corresponding legend item data | |||
const byDt = self.state.termdbConfig.assayAvailability?.byDt | |||
const order = value.class == 'CNV_loss' ? -2 : value.class.startsWith('CNV_') ? -1 : 0 | |||
const order = | |||
value.class == 'CNV_homozygous_deletion' |
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please create a reusable helper to convert cnv class to value and eliminate code dup
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thanks
Description
please also checkout to gdc branch: support_GDC_CNV_5Cats
Test with http://localhost:3000/example.gdc.matrix.html?cohort=Gliomas
Without VPN: show only CNV gain/loss
with qa-orange VPN: show all CNV categories
TODO: consider all CNV categories when computing top mutated genes
Checklist
Check each task that has been performed or verified to be not applicable.