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opain wants to merge 163 commits into from
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Dev #140

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1924aa0
Adding PRS-CSx functinoality and testing in opensnp
Jul 29, 2024
7498351
Completed benchmark using PRS-CSx in opensnp data, and added in x-win…
Aug 5, 2024
b7c4001
Added TL-PRS
Aug 19, 2024
cdc9950
Further edits to implement TLPRS
Aug 22, 2024
12c8cb2
Updates to multi-GWAS PGS methods
Aug 28, 2024
77ce41f
Merge branch 'dev' of github.com:opain/GenoPred into gwas_grouping
Sep 11, 2024
4db9fe7
Implementing BridgePRS
Sep 13, 2024
27f033c
Removed BridgePRS from absilable methods until implementation is comp…
Sep 13, 2024
65ff78b
Updating GenoUtils package
Sep 16, 2024
88141bb
Updated GenoUtils
Sep 16, 2024
70ac7e2
Fixed bug in DBSLMM when not using CHR 6
Sep 16, 2024
80ba773
Making updates to model_builder script and pipeline for crosspop
Sep 19, 2024
d24b418
Merge branch 'dev' into gwas_grouping
Sep 19, 2024
079ceb1
Added check that gwas_groups contains gwas in gwas_list, and increase…
Sep 23, 2024
f39d225
Updating model builder and crosspop analysis
Sep 23, 2024
0164cb4
Integrated target_pop specific findo_pseudo use in reports
Sep 25, 2024
498e9f8
Updates to model builder and crosspop analysis
Sep 25, 2024
b6dbdaa
Updates to pipeline for TLPRS
Sep 26, 2024
c7a2267
Updated model builder, and updated cross pop analysis
Sep 27, 2024
437e448
Added gwas_groups info to pipeline reports
Sep 28, 2024
f03f454
Updated docs to describe using multi-source PGS methods
Sep 28, 2024
0a40e38
Updating docs
Sep 28, 2024
0cab25e
Updates for cross pop analysis
Sep 30, 2024
896c92b
Updated target scoring to run sequentially for each chromosome to avo…
Sep 30, 2024
91db708
Restricting sig fig in score files to avoid uneccessary precision and…
Sep 30, 2024
1d99538
Added code to create reference data for LDpred2. Added functionality …
Oct 2, 2024
5cd9a5d
Extended timelimit for target scoring rule
Oct 2, 2024
9964db4
Added code to create LD reference data for LDpred2
Oct 9, 2024
75f18ce
Allowed LDpred2 to try a range of LD shrinkage values
Oct 9, 2024
a9a5d20
Included some config file checks, and updated cross population analys…
Oct 9, 2024
9a405b6
Updated default config to include gwas_groups
Oct 9, 2024
50b72ca
Updated document for LDpred2 ref creation
Oct 9, 2024
eda0062
Updated to model_builder
Oct 9, 2024
a776f50
Allowed for chr string in chr_name column of score file
Oct 11, 2024
6a0358e
Update to model_builder to remove duplicate features within each group
Oct 11, 2024
2283202
Avoided recalculating PGS for unchanged score files, unless target ge…
Oct 11, 2024
1c7dfd7
fixed bug in DBSLMM when SNP-h2 is low
Oct 11, 2024
4b49f50
Improved log when SNP-heritability is low
Oct 11, 2024
43ac4d0
Set to use pseudo model only in tlprs
Oct 11, 2024
9e38c80
Using config param for tlprs
Oct 11, 2024
934d52b
Added checked no duplicate names across gwas_list, score_list and gwa…
Oct 15, 2024
b2b8186
Improved find_pseudo command when using TLPRS
Oct 15, 2024
de0734a
Updated documentation regarding find_pseudo
Oct 15, 2024
89c6836
Added more detailed comparison of TLPRS
Oct 15, 2024
b949d49
Fixed bug in target scorer when score names are similar
Oct 15, 2024
028d868
Update to model_builder
Oct 15, 2024
562e45c
Added quickprs, sbayesrc, updated ldpred2 ref generation, added sanit…
Oct 21, 2024
60fdf04
Minor updates
Oct 29, 2024
4755a5a
Merge branch 'gwas_grouping' into dev
opain Oct 30, 2024
e37427d
Merge pull request #126 from opain/dev
opain Oct 30, 2024
ed44edb
Update dependencies.smk
opain Oct 30, 2024
c32721a
Typo correction in comment
Nov 1, 2024
87869b3
Selected GWAS for crosspop analysis
Nov 3, 2024
54e1a8b
Added quickprs_multi
Nov 4, 2024
727ba11
Added quickprs_multi
Nov 4, 2024
d817126
Edited PRS-CS, PRS-CSx, and X-Wing to stop as soon as an iteration of…
Nov 8, 2024
e949997
Added an error catch for SBayesRC
Nov 8, 2024
445b2dd
Created LDpred2 matrices from hgdp_1kg
Nov 8, 2024
e7cceca
Minor updates to crosspop analysis and addition of figure showing rel…
Nov 8, 2024
b2ab1a5
Set --use-conda and mamba as default for pipeline in config
Dec 4, 2024
c95564a
Removed attempt to set use-conda and mamba flag from config as it is …
Dec 4, 2024
57e7e05
Added continuous correction of PGS for ancestry. Testing required
Dec 4, 2024
6b93059
Allowed for TRANS population in read_pgs function
Dec 6, 2024
707fa1a
Updated pgs_methods.smk to allow for TRANS PGS
Dec 6, 2024
81934ff
Starting adding benchmark using simulated data from HAPNEST
Dec 6, 2024
dd0f08e
Added PGS correlation matrix and GWAS header interptetor to report
Dec 6, 2024
3cdcece
Show TRANS PGS coloured by population in sample report
Dec 9, 2024
11913d2
Updated read_pgs function to include pseudo_only option, and updated …
Dec 9, 2024
16fb7db
Included parameter to select ancestry adjustment approach, continuous…
Dec 9, 2024
cb3e096
Developing HAPNEST demo
Jan 3, 2025
14e55df
Added Rproj file
Jan 3, 2025
c83fbbb
Fixed plink_pca function when using plink1 files
Jan 3, 2025
b41369a
Slight tweak of night mode toggle
Jan 3, 2025
57378fd
Update to demo using HAPNEST simulation
Jan 3, 2025
01312f8
Fixed plink function when using plink1 as input
Jan 3, 2025
4b1c8b4
Minor edit to correlation matrix plot dimensions
Jan 3, 2025
07e17bb
Updated documentation
Jan 3, 2025
fd76a7a
Fixed bug in outlier detection when unrelated individuals are not spe…
Jan 4, 2025
fa4ccec
Making some notes on running on dnanexus
opain Jan 6, 2025
e77ca09
Minor updates to attempt on DNAnexus
opain Jan 7, 2025
8438985
Updating documentation
Jan 14, 2025
31627e9
Added some documentation on how to run on DNAnexus
Jan 14, 2025
a44d302
Merge pull request #132 from opain/run_on_dnanexus
opain Jan 14, 2025
14c2141
Added DNAnexus demo for UKB
Jan 15, 2025
bec106a
Merge pull request #133 from opain/run_on_dnanexus
opain Jan 15, 2025
adab860
Updated documentation for running on DNAnexus
Jan 20, 2025
748412c
Merge pull request #134 from opain/run_on_dnanexus
opain Jan 20, 2025
f16f5e0
Merge pull request #135 from opain/trans_pgs
opain Jan 20, 2025
2cc3e5c
Merge branch 'dev' into gwas_grouping
Jan 20, 2025
a083198
updates for cross pop methods
Jan 21, 2025
961b899
Updates to cross pop set up
Jan 21, 2025
f7fd4d2
Updates
Jan 21, 2025
d18e091
Updates
Jan 22, 2025
2f05853
Updates
Jan 22, 2025
98cec61
Rerunning UKB crosspop analysis
Jan 22, 2025
36cd06d
continuing crosspop analysis in ukb
Jan 22, 2025
fb75bb9
Changed it so update to configfile name doesnt trigger rerun. Should …
Jan 23, 2025
d4e5f8d
Updates
Jan 25, 2025
afb7dcd
Update
Jan 25, 2025
c8ba391
Updates
Jan 26, 2025
4591866
Added in model_builder_top1.R
Jan 28, 2025
87e911f
Update error catching in sbayesrc
Jan 28, 2025
28ac80f
Updates to crosspop analysis
Jan 29, 2025
ef36c72
Update
Jan 29, 2025
4a6f8e5
Updates
Jan 30, 2025
84977bb
Updates
Jan 31, 2025
ac2de83
Updates to reference for trans PGS, and some documentation updates.
Feb 4, 2025
44b6fee
Updated reference data for TRANS PGS
Feb 5, 2025
cf4fce3
Update to test data for TRANS PGS
Feb 5, 2025
8996338
Updated test_data
Feb 5, 2025
ea1d24d
Updates
Feb 7, 2025
212c700
Parallelised the TRANS PGS adjustment
Feb 7, 2025
4c94324
Avoided redundency in quickprs_multi
Feb 7, 2025
47a896a
Bug fix in quickprs_multi
Feb 7, 2025
59117e2
Updates
Feb 8, 2025
f5ea3b8
Updating quickprs to used adjusted LEOPARD weights
Feb 12, 2025
e136b2c
Updating integration of LEOPARD
Feb 12, 2025
6b98975
Updates
Feb 17, 2025
f9d7e05
Updates
Feb 18, 2025
0c3f761
Updates
Feb 20, 2025
4192f4d
Updates
Feb 25, 2025
d3f63be
Updates
Feb 25, 2025
c3cfcad
Updates
Feb 26, 2025
9ab33cb
Updates
Feb 28, 2025
bd20e07
Updates
Mar 4, 2025
fee3a86
Update
Mar 4, 2025
1b89f53
Update
Mar 4, 2025
5420883
Updates
Mar 7, 2025
8f07020
Updates
Mar 11, 2025
4f3d7bf
Updates
Mar 18, 2025
3e57a80
Updates
Mar 20, 2025
ff144bf
Updates
Mar 20, 2025
49859f1
Updates
Mar 24, 2025
56461dc
Updates
Mar 28, 2025
14990a8
Updates
Mar 31, 2025
f843000
setting up test data for multi-source methods, and fixed bug in quick…
Apr 6, 2025
329f78f
Updates
Apr 6, 2025
d03dbe9
Merge pull request #136 from opain/gwas_grouping
opain Apr 6, 2025
d2f2a91
preparing test_data
Apr 6, 2025
a27fd43
Updating test_data
Apr 6, 2025
b616750
Updating tests
Apr 6, 2025
8724058
Update to tests
Apr 6, 2025
ef4f317
Fixed reshape depracation issue
Apr 6, 2025
bc97e88
Update test-pipeline.R
opain Apr 7, 2025
d7a056e
Updates
Apr 10, 2025
375d011
Updates
Apr 21, 2025
eee0e43
Updating cross_pop for reviewer comments
Apr 29, 2025
924a93a
Updates for reviews
Apr 30, 2025
12ab6e5
Added google cookie notification
May 1, 2025
90a5377
Prepping for expanded reference
May 2, 2025
01c3f74
bridgeprs test
May 5, 2025
79febd0
Updates for reviews
May 9, 2025
df24ecf
Update for reviewer
May 12, 2025
21fa31e
Updates for reviewer
May 14, 2025
d9633e7
Updates
May 21, 2025
437fc15
Reverted documentation to released version
May 21, 2025
5217b82
Updates
May 22, 2025
b22b4a7
updates
Jun 6, 2025
0baf762
Updating documentation
Jun 6, 2025
5a605b2
Updated docs
Jun 12, 2025
d649541
Updated documentation
Jun 13, 2025
5f6c35e
Merge branch 'dev' into gwas_groups
Jun 13, 2025
93da8bf
Merge pull request #139 from opain/gwas_groups
opain Jun 13, 2025
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1 change: 1 addition & 0 deletions .github/workflows/run_quick_tests.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,7 @@ jobs:
run: |
Rscript -e "testthat::test_dir('pipeline/tests/testthat')"
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
SIF_FILE: ${{ env.SIF_FILE }}
BRANCH_NAME: ${{ env.BRANCH_NAME }}

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13 changes: 13 additions & 0 deletions GenoPred.Rproj
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Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
Version: 1.0

RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default

EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8

RnwWeave: Sweave
LaTeX: pdfLaTeX
352 changes: 0 additions & 352 deletions Scripts/PRS-CSx/PRS_CSx_plink2.R
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