Opened 7 months ago

Closed 7 months ago

#1519 closed enhancement (fixed)

Add support for using "bimodality_coefficient" as a test for allelic imbalance in ASCAT

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

Description

The bimodality_coefficient() is part of the mousetrap R package, so we need to update the container. We also need to implement this test in our modified ASCAT code on GitHub: https://github.com/nnordborg/ascat/tree/scanb

Change History (7)

comment:1 by Nicklas Nordborg, 7 months ago

In 7331:

References #1519: Add support for using "bimodality_coefficient" as a test for allelic imbalance in ASCAT

Updated the singularity definition file to also include the mousetrap R package.

Important changes in the ASCAT R package that are related to this: https://github.com/nnordborg/ascat/commit/52ecb1bb1cc3bd542cdb71fefc5d31d55f2f4b78

Last edited 7 months ago by Nicklas Nordborg (previous) (diff)

comment:2 by Nicklas Nordborg, 7 months ago

In 7332:

References #1519: Add support for using "bimodality_coefficient" as a test for allelic imbalance in ASCAT

Updated the ASCAT wrapper script with the new parameter.

comment:3 by Nicklas Nordborg, 7 months ago

In 7333:

References #1519: Add support for using "bimodality_coefficient" as a test for allelic imbalance in ASCAT

Updated the "Start ASCAT" wizard with support for the new parameter.

comment:4 by Nicklas Nordborg, 7 months ago

In 7334:

References #1519: Add support for using "bimodality_coefficient" as a test for allelic imbalance in ASCAT

Updated the confirmation wizard and case summary so that the imbalance test is displayed correctly.

comment:5 by Nicklas Nordborg, 7 months ago

In 7335:

References #1519: Add support for using "bimodality_coefficient" as a test for allelic imbalance in ASCAT

Removing code that was used for debugging.

comment:6 by Nicklas Nordborg, 7 months ago

In 7337:

References #1519: Add support for using "bimodality_coefficient" as a test for allelic imbalance in ASCAT

Change order of options.

comment:7 by Nicklas Nordborg, 7 months ago

Resolution: fixed
Status: newclosed
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