Opened 14 months ago

Closed 14 months ago

#1535 closed enhancement (fixed)

Generate more metrics from ASCAT

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.49.4
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

In the ASCAT package there is a function ascat.metrics() that generates more statistics. We should use this function and save the resulting information in a text file.

Some of the information should be imported as annotations:

  • n_segs: Number of copy-number segments
  • LOH: Fraction of the genome with LOH
  • GI: Genomic instability score

Change History (4)

comment:1 by Nicklas Nordborg, 14 months ago

In 7381:

References #1535: Generate more metrics from ASCAT

All metrics are now saved to the stats.txt file.

comment:2 by Nicklas Nordborg, 14 months ago

In 7382:

References #1535: Generate more metrics from ASCAT

Added a link to open the stats.txt file in the ASCAT confirmation wizard and on the page that display existing results.

comment:3 by Nicklas Nordborg, 14 months ago

Description: modified (diff)

comment:4 by Nicklas Nordborg, 14 months ago

Resolution: → fixed
Status: new → closed

In 7402:

Fixes #1535: Generate more metrics from ASCAT

Added three more annotations and import values to them after ASCAT analysis:

  • NumberOfSegments
  • LOH_fraction
  • GI_score
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