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Last updated: 2022-07-27

Checks: 2 0

Knit directory: mr_mash_test/

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.

Repository version: 4654738

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

The results in this page were generated with repository version 4654738. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

Unstaged changes:
    Modified:   analysis/tissue_sample_sizes.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
Rmd	4654738	Peter Carbonetto	2022-07-27	workflowr::wflow_publish("index.Rmd")
html	79c441c	Fabio Morgante	2022-05-10	Build site.
html	7964d16	Fabio Morgante	2022-05-10	Build site.
html	8ae4f90	Fabio Morgante	2022-05-10	Build site.
html	94e6521	Fabio Morgante	2022-05-10	Build site.
html	76f4680	Fabio Morgante	2022-05-10	Build site.
html	cddd2d7	Fabio Morgante	2021-11-27	Build site.
html	b9f7d67	Fabio Morgante	2021-11-27	Build site.
html	b8589a5	Fabio Morgante	2021-11-27	Build site.
html	4d7c1f2	Fabio Morgante	2021-11-27	Build site.
html	ef0d723	Fabio Morgante	2021-11-27	Build site.
html	9db563c	Fabio Morgante	2021-11-27	Build site.
html	b382d6d	Fabio Morgante	2021-11-24	Build site.
html	38c5a01	Fabio Morgante	2021-11-24	Build site.
html	0eb33fd	Fabio Morgante	2021-11-24	Build site.
Rmd	03602d2	Fabio Morgante	2021-11-24	Fix another bug
html	6faa215	Fabio Morgante	2021-11-12	Build site.
Rmd	759c3a5	Fabio Morgante	2021-11-12	Add description and fix a few things
html	5240e1c	Fabio Morgante	2021-11-12	Build site.
Rmd	164147e	Fabio Morgante	2021-11-12	Test new results documents
html	8093b84	Fabio Morgante	2021-06-14	Build site.
Rmd	3dfa242	Fabio Morgante	2021-06-14	Add comparison
html	2dcb898	Fabio Morgante	2021-05-11	Build site.
Rmd	9e3b05f	Fabio Morgante	2021-05-11	Add mr.mash vs smtlasso vs utmost
html	d8d1a3a	Fabio Morgante	2021-04-29	Build site.
Rmd	3942d02	Fabio Morgante	2021-04-29	Update all scenarios without missing Ys after fixing issues with DSC
html	4291f6b	Fabio Morgante	2021-04-25	Build site.
html	b8d7147	Fabio Morgante	2021-04-20	Build site.
Rmd	3081598	Fabio Morgante	2021-04-20	Update all scenarios with missing Ys after fixing issues with DSC and
html	b2c3824	fmorgante	2021-03-25	Build site.
html	cde23ac	fmorgante	2021-03-24	Build site.
Rmd	d5846a6	fmorgante	2021-03-24	Add investigation on the issue with larger r
html	f339f54	fmorgante	2021-03-24	Build site.
Rmd	cbdcee4	fmorgante	2021-03-24	Link the correct files
html	c1dee22	fmorgante	2021-03-24	Build site.
Rmd	8bc09c4	fmorgante	2021-03-24	Add all scenarios and improve text
html	20165dd	fmorgante	2021-03-23	Build site.
html	d442d10	fmorgante	2021-03-23	Build site.
Rmd	3ed1a81	fmorgante	2021-03-23	Add 1 causal tissue scenario with missing Y
html	880e867	fmorgante	2021-01-07	Build site.
html	d8b892a	fmorgante	2021-01-07	Build site.
Rmd	9b465e3	fmorgante	2021-01-07	Add shared effects scenario
html	2879e7a	fmorgante	2021-01-07	Build site.
Rmd	16c2741	fmorgante	2021-01-07	Add 2 blocks scenario
html	c73972e	fmorgante	2021-01-07	Build site.
html	c2f783e	fmorgante	2021-01-07	Build site.
Rmd	e80c8c7	fmorgante	2021-01-07	Add independent effects scenario
html	17d148d	fmorgante	2021-01-06	Build site.
Rmd	3d7ccdf	fmorgante	2021-01-06	Add 3 causal responses scenario
html	34010a9	fmorgante	2021-01-06	Build site.
html	ada87f4	fmorgante	2021-01-06	Build site.
html	11ab38f	fmorgante	2021-01-06	Build site.
html	cf00de2	fmorgante	2021-01-06	Build site.
html	ad676cc	fmorgante	2021-01-06	Build site.
Rmd	d8e690d	fmorgante	2021-01-06	Add singleton scenario with independent replicates
html	3ac4d65	fmorgante	2020-10-23	Build site.
Rmd	becde5f	fmorgante	2020-10-23	Add new scenarios
html	9d79f36	fmorgante	2020-10-22	Build site.
Rmd	8882669	fmorgante	2020-10-22	Update index
html	65d78b2	fmorgante	2020-10-22	Build site.
Rmd	ea2f1f3	fmorgante	2020-10-22	Add new scenario
html	aa1982b	fmorgante	2020-10-22	Build site.
html	b1d88f3	fmorgante	2020-10-22	Build site.
html	fd99070	fmorgante	2020-10-22	Build site.
html	1f6cf75	fmorgante	2020-10-22	Build site.
Rmd	9fe619a	fmorgante	2020-10-22	Add new results
html	df6c62c	fmorgante	2020-09-29	Build site.
html	f55e634	fmorgante	2020-09-28	Build site.
html	f797151	fmorgante	2020-09-28	Build site.
html	a34b486	fmorgante	2020-09-28	Build site.
html	7a34e29	fmorgante	2020-09-28	Build site.
html	0cfeb33	fmorgante	2020-09-28	Build site.
html	98989fe	fmorgante	2020-09-28	Build site.
html	d3995e4	fmorgante	2020-09-28	Build site.
html	a91280e	fmorgante	2020-09-28	Build site.
html	ec37fde	fmorgante	2020-09-28	Build site.
Rmd	d6974b3	fmorgante	2020-09-28	Add 3/10 causal responses results
html	2f036f9	fmorgante	2020-09-26	Build site.
html	e2b7e5d	fmorgante	2020-09-26	Build site.
Rmd	63758ce	fmorgante	2020-09-26	Add results with effects from mixture
Rmd	1acdd64	fmorgante	2020-09-25	Add first batch of new results
html	e59305a	fmorgante	2020-07-02	Build site.
html	c16a043	fmorgante	2020-07-02	Build site.
Rmd	fb4c660	fmorgante	2020-07-02	Add two_active_responses_issue_continued results
html	233be5c	fmorgante	2020-07-01	Build site.
Rmd	6cec9b6	fmorgante	2020-07-01	Fix formatting
html	701955c	fmorgante	2020-07-01	Build site.
Rmd	29d5be5	fmorgante	2020-07-01	Add mash vs mr.mash comparison
html	fb32d53	fmorgante	2020-06-05	Build site.
Rmd	b3c5072	fmorgante	2020-06-05	Add univariate results
html	01e3909	fmorgante	2020-06-03	Build site.
Rmd	33806cd	fmorgante	2020-06-03	Add dense scenario with larger sample size
html	42ec51c	fmorgante	2020-06-01	Build site.
Rmd	ceda278	fmorgante	2020-06-01	Add case study with dense scenario
html	e5a7adc	fmorgante	2020-05-27	Build site.
Rmd	6ccc7e2	fmorgante	2020-05-27	Fix typo
html	7dad46c	fmorgante	2020-05-27	Build site.
Rmd	465b10d	fmorgante	2020-05-27	Add case study with only two causal tissues out of five
html	3f8349c	fmorgante	2020-05-25	Build site.
html	9f85985	fmorgante	2020-05-25	Build site.
Rmd	3002ada	fmorgante	2020-05-25	Test glmnet comparison
html	24941d4	fmorgante	2020-05-20	Build site.
Rmd	d423390	fmorgante	2020-05-20	Update index
html	841c8bf	fmorgante	2020-05-20	Build site.
html	4263395	fmorgante	2020-05-20	Build site.
html	72c302a	fmorgante	2020-05-20	Build site.
html	a54eba5	fmorgante	2020-05-20	Build site.
Rmd	8f33ab9	fmorgante	2020-05-20	Test new set of results
html	ef2ad76	fmorgante	2020-04-28	Build site.
Rmd	9bdcd02	fmorgante	2020-04-28	Add highcorrX results
Rmd	187bb2d	fmorgante	2020-04-28	Add highcorrX results
html	3d61182	fmorgante	2020-04-28	Build site.
html	8ed3a7f	fmorgante	2020-04-28	Build site.
html	f2fa981	fmorgante	2020-04-28	Build site.
Rmd	51cea81	fmorgante	2020-04-28	Add newest results
html	e2c9550	fmorgante	2020-04-16	Build site.
Rmd	2e37a1d	fmorgante	2020-04-16	Add more results
html	161eea7	fmorgante	2020-04-16	Build site.
html	dd40784	fmorgante	2020-04-16	Build site.
html	8f4456e	fmorgante	2020-04-16	Build site.
Rmd	f6f65c4	fmorgante	2020-04-16	Fix index
html	422658e	fmorgante	2020-04-16	Build site.
Rmd	29dba0f	fmorgante	2020-04-16	Add indepX_lowcorrV_sharedB results
html	04f5485	fmorgante	2020-03-30	Build site.
html	cc50c05	fmorgante	2020-03-30	Build site.
html	378e278	fmorgante	2020-03-30	Build site.
html	40cd0cf	fmorgante	2020-03-30	Build site.
html	b48d34d	fmorgante	2020-03-30	Build site.
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html	f2c716e	fmorgante	2020-03-30	Build site.
html	8e7a5b5	fmorgante	2020-03-30	Build site.
html	4e9aad6	fmorgante	2020-03-30	Build site.
html	7911e81	fmorgante	2020-03-30	Build site.
html	e1707b2	fmorgante	2020-03-30	Build site.
html	f2451af	fmorgante	2020-03-29	Build site.
html	2fe7214	fmorgante	2020-03-29	Build site.
Rmd	d43e6a6	fmorgante	2020-03-29	Set current date automatically
html	dbf0d8e	fmorgante	2020-03-29	Build site.
html	c71dfff	fmorgante	2020-03-29	Build site.
html	796c93e	fmorgante	2020-03-29	Build site.
Rmd	ed9843a	fmorgante	2020-03-29	Add additional pages
html	b186ce3	fmorgante	2020-03-29	Build site.
Rmd	3b4bbc8	fmorgante	2020-03-29	Update Rmd files
Rmd	2c2c431	fmorgante	2020-03-28	Start workflowr project.

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This website includes analyses to assess the performance of mr.mash.

Results for meeting on 03/30/2020.

• Assessment of prediction accuracy.
• Assessment of convergence.

Results for meeting on 04/16/2020. Assessment of prediction accuracy and run time of mr.mash with different options in the following simulation scenarios:

• Independent predictors, shared effects, lowly correlated residuals.
• Independent predictors, independent effects, lowly correlated residuals.
• Correlated predictors, shared effects, lowly correlated residuals.
• Correlated predictors, independent effects, lowly correlated residuals.

Results for meeting on 04/30/2020. Assessment of prediction accuracy and run time of mr.mash with different options in the following simulation scenarios:

• Independent predictors, shared effects, lowly correlated residuals.
• Independent predictors, independent effects, lowly correlated residuals.
• Correlated predictors, shared effects, lowly correlated residuals.
• Correlated predictors, independent effects, lowly correlated residuals.
• Highly correlated predictors, shared effects, lowly correlated residuals.
• Highly correlated predictors, independent effects, lowly correlated residuals.

Results for meeting on 05/27/2020. Assessment of prediction accuracy and run time of mr.mash with different options against the multivariate versions of LASSO, Elastic Net, and Ridge regression in the following simulation scenarios:

• Independent predictors, shared effects, lowly correlated residuals.
• Independent predictors, independent effects, lowly correlated residuals.
• Correlated predictors, shared effects, lowly correlated residuals.
• Correlated predictors, independent effects, lowly correlated residuals.
• Highly correlated predictors, shared effects, lowly correlated residuals.
• Highly correlated predictors, independent effects, lowly correlated residuals.
• Case study with only two causal responses out of five total.

Results for meeting on 09/29/2020. Assessment of prediction accuracy and run time of mr.mash with different prior specifications against the multivariate versions of LASSO, Elastic Net, and Ridge regression in GTEx-like scenarios:

• Three scenarios for predictors correlation, two blocks of responses (shared effects within block), independent residuals.
• Independent predictors, three causal responses (shared effects) out of ten, independent residuals.

Results for meeting on 10/23/2020. Assessment of prediction accuracy and run time of mr.mash with different prior specifications against the multivariate version of LASSO, UTMOST, and univariate Elastic Net in simulations based on GTEx v8 genotypes:

• One causal response out of ten, independent residuals.
• Three causal responses (with shared effects) out of ten, independent residuals.
• Two blocks of responses (shared effects within block), independent residuals.
• Shared effects, independent residuals.
• Indpendent effects, independent residuals.

Results for meeting on 01/08/2021 (updated on 04/29/2021 after fixing seed issue in DSC and genotypes/expression issues in the rds files). Assessment of prediction accuracy and run time of mr.mash with different prior specifications against the multivariate version of LASSO, UTMOST, and univariate Elastic Net in simulations based on GTEx v8 genotypes with truly independent replicates:

• One causal response out of ten, independent residuals.
• Three causal responses (with shared effects) out of ten, independent residuals.
• Two blocks of responses (shared effects within block), independent residuals.
• Shared effects, independent residuals.
• Indpendent effects, independent residuals.

Results for meeting on 03/29/2021 (updated on 04/20/2021 after fixing seed issue in DSC and genotypes/expression issues in the rds files). Assessment of prediction accuracy and run time of mr.mash with different prior specifications against UTMOST, and univariate Elastic Net in simulations based on GTEx v8 genotypes with truly independent replicates and missing values in Y:

• One causal response out of ten, independent residuals.
• Three causal responses (with shared effects) out of ten, independent residuals.
• Two blocks of responses (shared effects within block), independent residuals.
• Shared effects, independent residuals.
• Indpendent effects, independent residuals.
• Table summarizing results above.

Results of GTEx v8 data analysis:

• GTEx tissue sample sizes
• 10 randomly sampled genes
• 1000 randomly sampled genes

Other investigations:

• Case study with dense scenarios.
• Case study with dense scenarios and larger sample size.
• Case study with dense scenarios and univariate analysis.
• mash vs mr.mash.
• Case study with only two causal responses out of six total.
• Case study with larger number of conditions.
• Comparison between mr.mash, sparse multi-task lasso, and UTMOST.