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Last updated: 2024-10-02

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Knit directory: multigroup_ctwas_analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

<<<<<<< HEAD Repository version: 03f2e81

======= Repository version: bb512bd

>>>>>>> 3473cf4b33f129329674a193b57926ae1c28dbdb

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

<<<<<<< HEAD The results in this page were generated with repository version 03f2e81. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files. ======= The results in this page were generated with repository version bb512bd. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files. >>>>>>> 3473cf4b33f129329674a193b57926ae1c28dbdb

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Untracked files:
    Untracked:  analysis/multi_group_compare_decidingweights_4traits.Rmd

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>>>>>>> 3473cf4b33f129329674a193b57926ae1c28dbdb
Unstaged changes:
    Modified:   analysis/simulation_summary.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
html	bb512bd	sq-96	2024-10-02	update
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Rmd	cc28c90	XSun	2024-09-05	updait
html	cc28c90	XSun	2024-09-05	updait
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Rmd	e59f1f2	XSun	2024-05-07	update
html	e59f1f2	XSun	2024-05-07	update
Rmd	a00c2c8	sq-96	2024-05-06	add single weight simulation
html	a00c2c8	sq-96	2024-05-06	add single weight simulation
Rmd	b0324db	sq-96	2024-02-05	update
html	b0324db	sq-96	2024-02-05	update
html	01aea33	kevinlkx	2024-01-19	Build site.
Rmd	86a0310	kevinlkx	2024-01-19	update index page
html	7a7c814	sq-96	2024-01-19	update
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html	2f6c0dd	sq-96	2023-12-30	update
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html	0a32579	sq-96	2023-12-30	update
Rmd	97049b2	XSun	2023-12-17	update
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html	4ec9466	sq-96	2023-12-13	update
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html	dce5552	sq-96	2023-12-13	update
html	fd8c5f2	kevinlkx	2023-12-07	Build site.
Rmd	b98fcd9	kevinlkx	2023-12-07	wflow_publish("analysis/index.Rmd")
Rmd	9a49925	sq-96	2023-12-05	update
html	9a49925	sq-96	2023-12-05	update
html	d2ccdfd	sq-96	2023-12-03	update
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html	43b79d7	kevinlkx	2023-11-29	Build site.
Rmd	4672c9e	kevinlkx	2023-11-29	added link with DENTIST result
Rmd	602e846	sq-96	2023-11-20	update histone weights
html	602e846	sq-96	2023-11-20	update histone weights
Rmd	23b5515	sq-96	2023-11-20	update apa results
html	23b5515	sq-96	2023-11-20	update apa results
html	9b57773	kevinlkx	2023-11-14	Build site.
Rmd	c062fd9	kevinlkx	2023-11-14	wflow_publish("analysis/index.Rmd")
Rmd	a406e50	XSun	2023-11-13	update
html	a406e50	XSun	2023-11-13	update
Rmd	ddf474a	Xiaotong Sun	2023-11-13	update
Rmd	909f2ad	XSun	2023-11-13	update
html	909f2ad	XSun	2023-11-13	update
html	f9cd866	sq-96	2023-11-12	Build site.
Rmd	66430f6	sq-96	2023-11-12	Start workflowr project.

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Data

GWAS, LD, expr_weights

6 modality weights from Munro et al.

Simulation results

• Simulation results

LD mismatch diagnosis

• LD mismatch diagnosis using SuSiE_RSS
• Detect LD mismatch for LDL and aFib using DENTIST vs. SuSiE_RSS
• Compare DENTIST and SuSiE_RSS for LD mismatch detection on example locus with manually changed z-scores
• Compare LD mismatch filterng on real data

Multi-tissue

Package V1.0

• Deciding the matching tissue
• Multi-tissue analysis, merging the LD blocks
• Validation
• Enrichment analysis – enriched pathways
• LDL ten tissues analysis link

Package V2.0

• Deciding the matching tissue

Single QTL analysis

Package V1.0

• APA QTL analysis link
• histone QTL analysis link

Package V2.0

• APA QTL analysis (using APA FUSION models by Chen et al.)

Region Merge

• Test region merge link

Multi omics and multi tissues analysis

package v1.0

• LDL - Liver and Adipose - Expression and Splicing link
• LDL - Multi contexts/types link

package v2.0

• 6 Traits, 5 tissues, eQTL + sQTL + apaQTL – load predicdb LD, eqtl, sqtl from predictdb; apa qtl from Chen et al
• 6 Traits, 5 tissues, eQTL + sQTL + apaQTL – compute ukbb LD, eqtl, sqtl from predictdb; apa qtl from Chen et al
• Summary for 6 Traits, 5 tissues, eQTL + sQTL + apaQTL – compute ukbb LD, eqtl, sqtl from predictdb; apa qtl from Chen et al
• 6 Traits, 5 tissues, eQTL + sQTL + apaQTL – compute ukbb LD, all weights are from Munro et al
• Summary for 6 Traits, 5 tissues, eQTL + sQTL + apaQTL – compute ukbb LD, all weights are from Munro et al

Deciding weights

Comparing results from Munro weights & predictdb weights

<<<<<<< HEAD
• IBD: predictdb eQTL + sQTL VS Munro 6 modalities – thin method V1
• IBD: predictdb eQTL + sQTL + Munro rsQTL + apaQTL VS all 8 weights – thin method V1
• IBD, LDL, SBP, WBC: predictdb eQTL / Munro eQTL / predictdb eQTL + sQTL / predictdb eQTL + sQTL + Munro rsQTL + apaQTL / all 8 weights
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• LDL + IBD: predictdb eQTL + sQTL VS Munro 6 modalities – thin method V2
• LDL + IBD: predictdb eQTL + sQTL VS Munro 6 modalities – thin method V1
• IBD: predictdb eQTL + sQTL + Munro rsQTL + apaQTL VS all 8 weights – thin method V2
• IBD: predictdb eQTL + sQTL + Munro rsQTL + apaQTL VS all 8 weights – thin method V1
>>>>>>> 3473cf4b33f129329674a193b57926ae1c28dbdb

LDL examples

package v2.0

• Predictdb sQTL from Liver
• Predictdb eQTL&sQTL from Liver
• Comparing single-group & multi-group for LDL – old PIP combining function
• Comparing single-group & multi-group for LDL - new PIP combining function
• Comparing different PIP combining functions

Old simulation results

• seven uncorrelated tissues simulations link
• seven correlated tissues simulations link
• seven correlated brain tissues simulations link
• Single weight simulations link
• Four expression traits simulations link
• E and S three tissues simulations link