Opened 6 months ago

Closed 6 months ago

#1515 closed enhancement (fixed)

Pick up the "Non-aberrant" flag from ASCAT result and import as an annotation in BASE

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.49.1
Component: net.sf.basedb.reggie Keywords:
Cc:

Description


Change History (5)

comment:1 by Nicklas Nordborg, 6 months ago

In 7324:

References #1515: Pick up the "Non-aberrant" flag from ASCAT result and import as an annotation in BASE

Added a --debug option to the run_ascat.R script that save the ascat.bc and ascat.output objects to .Rdata files. This will be useful for manual inspection and testing without having to re-run everything before every time.

comment:2 by Nicklas Nordborg, 6 months ago

In 7325:

References #1515: Pick up the "Non-aberrant" flag from ASCAT result and import as an annotation in BASE

Saving the NonAberrant flag to the stats.txt file. It is outputted as a 0/1 value.

comment:3 by Nicklas Nordborg, 6 months ago

In 7326:

References #1515: Pick up the "Non-aberrant" flag from ASCAT result and import as an annotation in BASE

Created the NonAberrant annotation type. It can have values "Yes" or "No", but we only set the "Yes" value if the flag is present in the ASCAT output.

comment:4 by Nicklas Nordborg, 6 months ago

In 7327:

References #1515: Pick up the "Non-aberrant" flag from ASCAT result and import as an annotation in BASE

Display the "Non-aberrant" flag in the confirmation wizard and case summary.

comment:5 by Nicklas Nordborg, 6 months ago

Resolution: fixed
Status: newclosed
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