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GDC support 5-category cnv #2545

Merged
merged 3 commits into from
Dec 30, 2024
Merged

GDC support 5-category cnv #2545

merged 3 commits into from
Dec 30, 2024

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congyu-lu
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@congyu-lu congyu-lu commented Dec 24, 2024

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.

  • Tests: added and/or passed unit and integration tests, or N/A
  • Todos: commented or documented, or N/A
  • Notable Changes: updated release.txt, prefixed a commit message with "fix:" or "feat:", added to an internal tracking document, or N/A

@congyu-lu congyu-lu linked an issue Dec 24, 2024 that may be closed by this pull request
@@ -282,6 +282,7 @@ mclass[mclasssv] = {
key: mclasssv
}

//TODO:CNV_amp should be repalced with CNV_gain to avoid confusion with CNV amplification (CNV_amplification) below
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@xzhou82 xzhou82 Dec 30, 2024

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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
}

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

@@ -223,7 +223,18 @@ export function setGeneVariantCellProps(cell, tw, anno, value, s, t, self, width

// 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

@xzhou82 xzhou82 merged commit 0af9d0b into master Dec 30, 2024
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@xzhou82 xzhou82 deleted the support_GDC_CNV_5Cats branch December 30, 2024 20:14
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gdc: support 5-category cnv
2 participants