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Last updated: 2023-06-11

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Knit directory: causal-TWAS/

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Repository version: c440306

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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
Rmd	c440306	simingz	2023-06-10	more settings for low SNP PVE
html	c440306	simingz	2023-06-10	more settings for low SNP PVE
Rmd	972fe6d	simingz	2023-06-05	low PVE simulation bug fix
html	972fe6d	simingz	2023-06-05	low PVE simulation bug fix
Rmd	de95a10	simingz	2023-05-08	110k simulation
html	de95a10	simingz	2023-05-08	110k simulation
Rmd	d76d5c4	simingz	2023-04-20	more simulation settings for low SNP PVE
html	d76d5c4	simingz	2023-04-20	more simulation settings for low SNP PVE
Rmd	ca90eff	simingz	2021-07-31	simulation paper figures
html	ca90eff	simingz	2021-07-31	simulation paper figures
Rmd	fe0e8f8	simingz	2021-05-09	added smr-heidi results, scripts matching v0.1.25
html	fe0e8f8	simingz	2021-05-09	added smr-heidi results, scripts matching v0.1.25
Rmd	b096cb2	simingz	2021-04-04	add coloc
html	b096cb2	simingz	2021-04-04	add coloc
Rmd	5cca4e3	simingz	2021-03-25	snp harmonization notes
html	5cca4e3	simingz	2021-03-25	snp harmonization notes
Rmd	3dd8cb2	simingz	2021-02-19	mix normal simulate phenotype
html	3dd8cb2	simingz	2021-02-19	mix normal simulate phenotype
Rmd	68d891f	simingz	2021-01-26	ctwas para results
html	68d891f	simingz	2021-01-26	ctwas para results
html	fd9b304	simingz	2020-11-18	index
html	447a401	simingz	2020-11-13	pip cali
html	547abc4	simingz	2020-10-30	logBF
Rmd	f9c55de	simingz	2020-10-30	log bayes factor
html	f9c55de	simingz	2020-10-30	log bayes factor
html	bf57f32	simingz	2020-10-24	qqplot
Rmd	6526634	simingz	2020-10-23	filtered samples s40.22
html	6526634	simingz	2020-10-23	filtered samples s40.22
Rmd	fc1e98d	simingz	2020-10-20	small pvalues
Rmd	c2dee2c	simingz	2020-10-14	wg susieI
html	c2dee2c	simingz	2020-10-14	wg susieI
Rmd	4d39fd6	simingz	2020-09-14	susieI plots
html	4d39fd6	simingz	2020-09-14	susieI plots
Rmd	c989c96	simingz	2020-09-08	pretty plot for Xin’s grant
Rmd	bb0bce0	simingz	2020-09-03	susie prior
html	bb0bce0	simingz	2020-09-03	susie prior
Rmd	86681eb	simingz	2020-08-28	susieI all regions
html	86681eb	simingz	2020-08-28	susieI all regions
Rmd	846fb96	simingz	2020-08-14	susieI
html	846fb96	simingz	2020-08-14	susieI
Rmd	2216650	simingz	2020-08-06	Remove ignored files
html	2216650	simingz	2020-08-06	Remove ignored files
Rmd	75d7755	simingz	2020-08-05	visual chr17to22
html	75d7755	simingz	2020-08-05	visual chr17to22
Rmd	b6132ab	simingz	2020-08-05	visual chr17to22
html	b6132ab	simingz	2020-08-05	visual chr17to22
Rmd	f6ea15c	simingz	2020-08-04	change sa2 grid
html	f6ea15c	simingz	2020-08-04	change sa2 grid
html	537def8	simingz	2020-07-24	chr17:22
Rmd	e0835ef	simingz	2020-07-24	chr17:22
Rmd	89b90ad	simingz	2020-07-24	chr17:22
html	89b90ad	simingz	2020-07-24	chr17:22
Rmd	c00bcb1	simingz	2020-06-24	SUSIE examples
html	c00bcb1	simingz	2020-06-24	SUSIE examples
Rmd	fdd6e55	simingz	2020-06-24	susie examples
html	fdd6e55	simingz	2020-06-24	susie examples
Rmd	d3e7ba5	simingz	2020-06-24	susie more examples
html	d3e7ba5	simingz	2020-06-24	susie more examples
Rmd	4188e0a	simingz	2020-06-24	susie more examples
html	4188e0a	simingz	2020-06-24	susie more examples
html	de12f19	simingz	2020-06-20	reduce mr.ash memory/mr.ashs
Rmd	f41a1de	simingz	2020-06-18	logging and more weights for chr22
html	f41a1de	simingz	2020-06-18	logging and more weights for chr22
Rmd	8708f04	simingz	2020-06-11	SUSIE
html	8708f04	simingz	2020-06-11	SUSIE
html	e69753c	simingz	2020-06-11	after clean
Rmd	3a24c5e	simingz	2020-06-11	plotly
html	3a24c5e	simingz	2020-06-11	plotly
Rmd	8f01adb	simingz	2020-05-28	mr.ash2s
html	8f01adb	simingz	2020-05-28	mr.ash2s
Rmd	e417c92	simingz	2020-05-20	test mr.ash2
html	e417c92	simingz	2020-05-20	test mr.ash2
Rmd	8c5b557	simingz	2020-05-20	test mr.ash2
html	8c5b557	simingz	2020-05-20	test mr.ash2
Rmd	8294257	simingz	2020-05-19	test mr.ash
html	8294257	simingz	2020-05-19	test mr.ash
Rmd	ec20419	simingz	2020-04-16	veb-boost-repo
html	ec20419	simingz	2020-04-16	veb-boost-repo
Rmd	f327bca	simingz	2020-04-12	mr.ash description
html	f327bca	simingz	2020-04-12	mr.ash description
Rmd	83288ad	simingz	2020-03-31	sparse model description
html	83288ad	simingz	2020-03-31	sparse model description
Rmd	af533ec	simingz	2020-03-27	veb-boost reference
html	af533ec	simingz	2020-03-27	veb-boost reference
html	c6535ef	simingz	2020-03-25	fix results display bug
Rmd	e86023b	simingz	2020-03-25	fix results display bug
Rmd	2ae8625	simingz	2020-03-24	polygenic done
Rmd	a618a44	simingz	2020-03-13	v1.0 simulate expression using separate data 20191127
html	a618a44	simingz	2020-03-13	v1.0 simulate expression using separate data 20191127
html	dcd5252	simingz	2019-11-07	simulate description
Rmd	f7be05a	simingz	2019-11-05	gemma
html	56ba4ae	simingz	2019-11-03	add git icon
Rmd	68e228f	simingz	2019-11-03	model and Xin’s simulation
html	68e228f	simingz	2019-11-03	model and Xin’s simulation

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Model

• Polygenic model
• Sparse model
• mr.ash model

Data

• SNP data harmonization notes

Simulations

Proof of concept

• Proof of concept for this project using a single gene’s data

Test polygenic model

Using WTCCC data

• Test polygenic model 1

• Test polygenic model 2: use imputed expression

Test mr.ash

Using UKbiobank data (chr22)

• Test mr.ash performance: only SNP effect

Test mr.ash2s

A simplified version (mr.ash2) of Veb_boost: interative update of two mr.ash components

• Using some simple data

• Using UKbiobank data (chr22)

A simplified version (mr.ash2s): interative update of two mr.ash components, now including updates of sigma2 in each iteration and initiate with mr.ash for all.

• Using some simple data

• Using UKbiobank data (chr22), fusion weights YFS

• Using UKbiobank data (chr22), fusion weights Adipose subcutaneous

• Using UKbiobank data (chr22), weights of H3K27 from Xiaotong

Test SUSIE for fine-mapping

• Using UKbiobank data (chr22), fusion weights YFS, SUSIE L=1

• Using UKbiobank data (chr22), fusion weights YFS, SUSIE L=2

• Using UKbiobank data (chr22), fusion weights YFS, SUSIE L=3

• Using UKbiobank data (chr22), fusion weights Adipose, L=1

• Using UKbiobank data (chr22), fusion weights Adipose, L=2

• Using UKbiobank data (chr22), fusion weights Adipose, L=3

Summarize cTWAS results

We compare cTWAS results with other methods, summarizing results over multiple simulation runs.

• Using UKbiobank data (chr22), fusion weights Adipose
• Using UKbiobank data (chr22), fusion weights Adipose, setting 2
• Using UKbiobank data (chr17:22), fusion weights Adipose
• Using UKbiobank data (chr17:22), fusion weights Adipose, using smaller sa2 grid in mr.ash
  • Visualization

SUSIE iterative

• Using UKbiobank data (chr17:22), fusion weights Adipose

• Using UKbiobank data (chr17:22), fusion weights Adipose, test prior’s effect for susie

• Using UKbiobank data (whole genome), fusion weights Adipose

  • Visualization

ctwas package

Test the summary statistics version of the ctwas algorithm. Now provided as a R package.

Using normal distribution as prior distribution for causal effects

• Using UKbiobank data (22k samples), fusion weights Adipose

• Using UKbiobank data (22k samples), fusion weights Adipose, in-sample LD

• Using UKbiobank data (45k samples), fusion weights Adipose

• Using UKbiobank data (110k samples), fusion weights Adipose

• Using UKbiobank data (45k samples), fusion weights Adipose, more settings with low SNP PVE

• Using UKbiobank data (110k samples), fusion weights Adipose, more settings with low SNP PVE

• Visualization

Using normal mixture distribution as prior distribution for causal effects

• Using UKbiobank data (22k samples), fusion weights Adipose

• Using UKbiobank data (45k samples), fusion weights Adipose

Paper

• Simulation figures

Related software

• VEB-boost
  • Problem description
  • Andrew’s software and workflowr website
• mr.ash
  • mr.ash package
  • mr.ash workflowr website