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Use NP consistently in download tab #10789

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inodb opened this issue May 9, 2024 · 2 comments · May be fixed by cBioPortal/cbioportal-frontend#5057
Open

Use NP consistently in download tab #10789

inodb opened this issue May 9, 2024 · 2 comments · May be fixed by cBioPortal/cbioportal-frontend#5057
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@inodb
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inodb commented May 9, 2024 •
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For mutations data it is currently listed as NS (not sequenced) instead of NP (not profiled), but for CNA and SV it shows NP. Not profiled and not sequenced are synonyms. See this link:

image

e.g. mut:

DY_ID	SAMPLE_ID	SOS1	EGFR
msk_impact_2017	P-0000901-T01-IM3	NS	WT

vs cna:

STUDY_ID	SAMPLE_ID	SOS1	EGFR
msk_impact_2017	P-0000901-T01-IM3	NP	0

vs SV:

STUDY_ID	SAMPLE_ID	SOS1	EGFR
msk_impact_2017	P-0000901-T01-IM3	NP	NA

Discussion point: should SV also show WT like mut?
@vkonga
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vkonga commented Aug 6, 2024

Hi @inodb. As I understood, in mutations column (EGFR values should change to NP). I am interested to work on this good first issue.

@arishta-dev
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hi @inodb I have put up a PR to solve this issue:
please review cBioPortal/cbioportal-frontend#5057
Thanks!

@arishta-dev arishta-dev linked a pull request Nov 28, 2024 that will close this issue
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#10789 Modified EFGR values for Mutations in Download tab arishta-dev/cbioportal-frontend
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@inodb @vkonga @arishta-dev