#1419 closed task (fixed)

Methylation beta-analysis wizard

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: Reggie v4.41
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

Implement a wizard that calculate beta-values for methylation bioassays.

See ticket #1418 for information about importing information about the methylation processing and items. Since it is likely that we may do more of this type of analysis in the future it was decided that the actual analysis that create beta-values should be implemented as a wizard. The wizard should assume that DNA aliquots, BeadChip information and Methylation items have been imported as outlined in #1418.

The wizard will then start jobs on the new (container-based) cluster for running the Minfi pipeline that create beta-values, some PDF plots and other statistics for each sample.

Change History (20)

comment:1 by Nicklas Nordborg, 19 months ago

In 6867:

References #1419: Methylation beta-analysis wizard

Added a new section on the index page for "Other analysis" with a single subsection "Methylation".

comment:2 by Nicklas Nordborg, 19 months ago

In 6868:

References #1419: Methylation beta-analysis wizard

Added an item list "Methylation beta-analysis" for Methylation derived bioassays that should be analyzed with the beta pipeline.

comment:3 by Nicklas Nordborg, 19 months ago

In 6869:

References #1419: Methylation beta-analysis wizard

Added a wizard for selecting Methylation items for beta-analysis. The analysis is not yet implemented.

comment:4 by Nicklas Nordborg, 19 months ago

In 6870:

References #1419: Methylation beta-analysis wizard

Added a job creator implementation. It should be able to register and submit jobs to the cluster, but there is no script yet so the jobs will always fail.

comment:5 by Nicklas Nordborg, 19 months ago

In 6871:

References #1419: Methylation beta-analysis wizard

Added a simple script that so far only copy the IDAT files to the correct location in the project-archive directory.

comment:6 by Nicklas Nordborg, 19 months ago

In 6872:

References #1419: Methylation beta-analysis wizard

Added a conteiner definition for the Minfo R package that should be used for the beta value calculations.

comment:7 by Nicklas Nordborg, 19 months ago

In 6874:

References #1419: Methylation beta-analysis wizard

The R script now report progress to Reggie.

comment:8 by Nicklas Nordborg, 18 months ago

In 6875:

References #1419: Methylation beta-analysis wizard

Updated the R script to output a file with QC values and other measurements.

comment:9 by Nicklas Nordborg, 18 months ago

In 6876:

References #1419: Methylation beta-analysis wizard

Added a lot of annotations for storing the qc values.

comment:10 by Nicklas Nordborg, 18 months ago

In 6877:

References #1419: Methylation beta-analysis wizard

Added thumbnails of the beta adjustment plot to the derived bioassay list and view page for Methylation items.

comment:11 by Nicklas Nordborg, 18 months ago

In 6878:

References #1419: Methylation beta-analysis wizard

Added a flag annotation for recording some rare qc problems.

comment:12 by Nicklas Nordborg, 18 months ago

In 6879:

References #1419: Methylation beta-analysis wizard

Started with the confirmation wizard. It displays some information from the analysis and options for re-analyze failed jobs or confirm. Registration of the results is not yet implemented.

comment:13 by Nicklas Nordborg, 18 months ago

In 6880:

References #1419: Methylation beta-analysis wizard

Implemented confirmation and re-scheduling of finished beta-analysis jobs.

comment:14 by Nicklas Nordborg, 18 months ago

In 6881:

References #1419: Methylation beta-analysis wizard

Implemented auto-confirmation.

comment:15 by Nicklas Nordborg, 18 months ago

In 6882:

References #1419: Methylation beta-analysis wizard

Added methylation information to the case summary.

comment:16 by Nicklas Nordborg, 18 months ago

In 6883:

References #1419: Methylation beta-analysis wizard

Fixed documentation of container definition file.

comment:17 by Nicklas Nordborg, 18 months ago

In 6884:

References #1419: Methylation beta-analysis wizard

Since the run time for a job is ~1-2 minutes, we can decrease the interval between starting jobs from 30 to 5 seconds.

comment:18 by Nicklas Nordborg, 18 months ago

In 6885:

References #1419: Methylation beta-analysis wizard

Modified help text for auto-confirm.

comment:19 by Nicklas Nordborg, 18 months ago

In 6886:

References #1419: Methylation beta-analysis wizard

Adding a reference to the original script and authors.

comment:20 by Nicklas Nordborg, 18 months ago

Resolution: fixed
Status: newclosed
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