Adding arm-level CNA data

[jjgao]

Just wanted to capture the idea - this is not a priority.

• import the data as generic assay data Re-curate arm-level CNA as discrete generic assay data datahub#1308
• (implement as part of discrete generic assay) add arm-level cna to OncoPrint (gain and hetloss should be displayed by default unlike gene-level cna), Plots, Study View, Download

future tasks:

• (implement as part of discrete generic assay) add arm-level cna to enrichments tab.
• (implement as part of discrete generic assay) add a new table "Arm-level CNAs" in study view.
• create another profile types Arm-level copy number alteration in query interface
• allow user to type 1p or 1p:gain or 1p:hetloss in gene box for querying
• add arm-level CNAs to the CNA table in patient view?
• update documentation, including oql, faq, data format
• add to Cancer Types Summary tab when it's possible to query
• add to Mutual Exclusivity tab when it's possible to query

@cBioPortal/product

[AndyBlake]

Second this - We end up loading it as sample data for all the arms which is perhaps less than ideal from a ui point of view.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[jjgao]

unstale

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[AndyBlake]

Unstale

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[dippindots]

Modified description:

• Checked finished items
• Move enrichments and new study view table "Arm-level CNAs" into future tasks

CC: @jjgao

[jjgao]

@dippindots I removed the items related to query arm-level cna data. I think the benefit may not justify the cost to implement that.

[dippindots]

@jjgao Thanks!