replace code for rpy2 in correlation matrix using gn3 functions #597
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Dear Alex,
Does this fix our problem with GTEx HBB transcript correlation compute?
On Tue, Aug 10, 2021 at 7:34 PM Alexander Kabui ***@***.***> wrote:
Description
this code primarily replaces ryp2 code used in correlation matrix module
for computing pca
- also replaces some stats functions with one provided by numpy
- refactored codebase for correlation matrix module can also be found
in this pr (genenetwork/genenetwork3#23
<genenetwork/genenetwork3#23>) and should be
replace in a different PR
How should this be tested? Any background context you want to provide? What
are the relevant pivotal tracker stories? Screenshots (if appropriate)
Questions
------------------------------
You can view, comment on, or merge this pull request online at:
#597
Commit Summary
- Replace code for processing factor loadings
- delete r code
- Replace code for computing zscores
- Replace code for computing and sorting eigens
- Delete ununsed functions
- delete unused imports
File Changes
- *M* wqflask/wqflask/correlation_matrix/show_corr_matrix.py
<https://github.com/genenetwork/genenetwork2/pull/597/files#diff-331597ece32909ad405f738abb686cd66bf15c5ec5474c187388686193327416>
(115)
Patch Links:
- https://github.com/genenetwork/genenetwork2/pull/597.patch
- https://github.com/genenetwork/genenetwork2/pull/597.diff
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--
Rob
Robert W. Williams, Ph.D.
Chair: Department of Genetics, Genomics and Informatics
University of Tennessee Health Science Center
71 S Manassas St, Memphis TN 38103-3310, TSRB Room 405
Tele/Cell: 901 604 4752
EMAIL: ***@***.*** or ***@***.***
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Hi @robwwilliams, This Pr replaces rpy2 used for principal component analysis using python code in gn3.As for the hanging correlations fixed the |
Alexanderlacuna
changed the title
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Great. Thanks Alex.
…On Wed, Aug 11, 2021 at 1:15 AM Alexander Kabui ***@***.***> wrote:
Hi @robwwilliams <https://github.com/robwwilliams>, This Pr replaces rpy2
used for principal component analysis using python code in gn3.As for the
hanging correlations fixed the
the issue here:(genenetwork/genenetwork3#34
<genenetwork/genenetwork3#34>) .
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--
Rob
Robert W. Williams, Ph.D.
Chair: Department of Genetics, Genomics and Informatics
University of Tennessee Health Science Center
71 S Manassas St, Memphis TN 38103-3310, TSRB Room 405
Tele/Cell: 901 604 4752
EMAIL: ***@***.*** or ***@***.***
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Ping @Alexanderlacuna is this ready for merging? Any clean-up required? |
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@BonfaceKilz am actually doing cleanup on this PR. coz currently it does so many things needs to break it into smaller chunks. |
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@BonfaceKilz this is PR is related to genenetwork/genenetwork3#23 in gn3 |
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Alexander Kabui ***@***.***>
anaandika:
@BonfaceKilz this is PR is related to
genenetwork/genenetwork3#23
in gn3
Cool. Let me know when it's ready. A gentle probe
on e-mail or Matrix will suffice ;)
…--
Bonface M. K.
D4F09EB110177E03C28E2FE1F5BBAE1E0392253F (hkp://keys.gnupg.net)
Free Software Activist
Humble GNU Emacs User | Bearer of scheme-y parens
Curator: <https://upbookclub.com> | Twitter: @BonfaceKilz
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Description
this code primarily replaces ryp2 code used in correlation matrix module for computing pca
How should this be tested?
Any background context you want to provide?
What are the relevant pivotal tracker stories?
Screenshots (if appropriate)
Questions