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  1. IGB
  2. IGBF-3191

Compute PSI for splicing choice outcomes

        Details

        • Type: Task
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
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          Description

          Using output from TabulateSplicingSupport, compute PSI for each difference region, Ga vs. Gp comparison, in every sample.

          How can PSI capture the scale of the observation, the population size of the sequence alignment evidence?

          Maybe we can:

          • Encode depth of sequencing per choices by using significant digits.

          For example:

          PSI of 0.2341 means the outcome of a splicing choice (a sequence alignment) was observed at least 10,000 times.

          Does R allow this type of thing?

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              ann.loraine Ann Loraine created issue -
              ann.loraine Ann Loraine made changes -
              Field Original Value New Value
              Epic Link IGBF-2993 [ 21429 ]
              ann.loraine Ann Loraine made changes -
              Sprint Fall 3 2022 Sep 26 [ 155 ]
              ann.loraine Ann Loraine made changes -
              Sprint Fall 3 2022 Sep 26 [ 155 ] Fall 3 2022 Sep 26, Fall 4 2022 Oct 10 [ 155, 156 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              ann.loraine Ann Loraine made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              ann.loraine Ann Loraine made changes -
              Status In Progress [ 3 ] To-Do [ 10305 ]
              ann.loraine Ann Loraine made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
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              ann.loraine Ann Loraine added a comment -

              Made new branch with first draft of PSI-computing code:

              [IGBF-391 fba09a8] IGBF-3191 Compute PSI
 1 file changed, 81 insertions(+)
 create mode 100644 TabulateSplicingSupport/ComputePercentSplicedIn_1.Rmd
local aloraine$ git push origin IGBF-3191
Enumerating objects: 12, done.
Counting objects: 100% (12/12), done.
Delta compression using up to 16 threads
Compressing objects: 100% (7/7), done.
Writing objects: 100% (7/7), 1.43 KiB | 1.43 MiB/s, done.
Total 7 (delta 5), reused 0 (delta 0)
remote: 
remote: Create pull request for IGBF-3191:
remote:   https://bitbucket.org/aloraine/splicing-analysis/pull-requests/new?source=IGBF-3191&t=1
remote: 
To bitbucket.org:aloraine/splicing-analysis.git
 * [new branch]      IGBF-3191 -> IGBF-3191
              Show
              ann.loraine Ann Loraine added a comment - Made new branch with first draft of PSI-computing code: [IGBF-391 fba09a8] IGBF-3191 Compute PSI 1 file changed, 81 insertions(+) create mode 100644 TabulateSplicingSupport/ComputePercentSplicedIn_1.Rmd local aloraine$ git push origin IGBF-3191 Enumerating objects: 12, done. Counting objects: 100% (12/12), done. Delta compression using up to 16 threads Compressing objects: 100% (7/7), done. Writing objects: 100% (7/7), 1.43 KiB | 1.43 MiB/s, done. Total 7 (delta 5), reused 0 (delta 0) remote: remote: Create pull request for IGBF-3191: remote: https: //bitbucket.org/aloraine/splicing-analysis/pull-requests/ new ?source=IGBF-3191&t=1 remote: To bitbucket.org:aloraine/splicing-analysis.git * [ new branch] IGBF-3191 -> IGBF-3191
              ann.loraine Ann Loraine made changes -
              Status In Progress [ 3 ] To-Do [ 10305 ]
              nfreese Nowlan Freese made changes -
              Sprint Fall 3 2022 Sep 26, Fall 4 2022 Oct 10 [ 155, 156 ] Fall 3 2022 Sep 26, Fall 4 2022 Oct 10, Fall 5 2022 Oct 24 [ 155, 156, 157 ]
              nfreese Nowlan Freese made changes -
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              ann.loraine Ann Loraine added a comment -

              Tabling this pending deploy of data onto a quickload.

              Show
              ann.loraine Ann Loraine added a comment - Tabling this pending deploy of data onto a quickload.
              ann.loraine Ann Loraine made changes -
              Sprint Fall 3 2022 Sep 26, Fall 4 2022 Oct 10, Fall 5 2022 Oct 24 [ 155, 156, 157 ] Fall 3 2022 Sep 26, Fall 4 2022 Oct 10 [ 155, 156 ]
              nfreese Nowlan Freese made changes -
              Sprint Fall 3 2022 Sep 26, Fall 4 2022 Oct 10 [ 155, 156 ] Fall 3 2022 Sep 26, Fall 4 2022 Oct 10, Spring 3 2023 Jan 30 [ 155, 156, 163 ]
              nfreese Nowlan Freese made changes -
              Rank Ranked higher
              ann.loraine Ann Loraine made changes -
              Sprint Fall 3 2022 Sep 26, Fall 4 2022 Oct 10, Spring 3 2023 Feb 1 [ 155, 156, 163 ] Fall 3 2022 Sep 26, Fall 4 2022 Oct 10 [ 155, 156 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              ann.loraine Ann Loraine made changes -
              Assignee Ann Loraine [ aloraine ]

                People

                • Assignee:
                  Unassigned
                  Reporter:
                  ann.loraine Ann Loraine
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                  Dates

                  • Created:
                    Updated: