Multivariate Bayesian variable selection regression

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mvSuSiE benchmark results summary

Commands generated the results in this notebook can be found here.

Credible sets

Without missing data

%cd /home/gaow/GIT/mvarbvs/dsc/mnm_prototype/mnm_20210310

/project2/mstephens/gaow/mvarbvs/dsc/mnm_prototype/mnm_20210310

readRDS("mnm_20210310.cs_summary.rds")$table

	simulate	method	total	overlap_cs	size	purity	power	fdr	cs_correlation	size_cond_cs	purity_cond_cs	power_cond_cs	fdr_cond_cs	converged
9	artificial_mixture	mnm_shared+flash_residual	431	0	6.75	0.9894560	0.266	0.035	0.1915794	6.75	0.9894560	1.000	0.039	1
10	artificial_mixture	mnm_shared+oracle_residual	455	0	6.00	0.9933845	0.275	0.042	0.1785286	6.00	0.9933845	1.000	0.046	1
3	artificial_mixture	mnm_identity+flash_residual	704	0	5.00	0.9924977	0.424	0.045	0.1799465	4.00	0.9964978	0.535	0.036	1
4	artificial_mixture	mnm_identity+oracle_residual	728	0	4.50	0.9942843	0.430	0.059	0.1811708	3.75	1.0000000	0.538	0.044	1
1	artificial_mixture	mnm_ed+flash_residual	720	0	5.00	0.9938684	0.439	0.029	0.1860816	4.00	0.9968229	0.686	0.021	1
2	artificial_mixture	mnm_ed+oracle_residual	734	0	4.00	0.9950575	0.447	0.031	0.1898279	3.50	1.0000000	0.686	0.025	1
5	artificial_mixture	mnm_naive+flash_residual	814	42	5.00	0.9900349	0.467	0.036	0.3289438	4.00	0.9948460	0.600	0.024	1
6	artificial_mixture	mnm_naive+oracle_residual	833	42	5.00	0.9924091	0.474	0.043	0.3290083	4.00	0.9974383	0.594	0.025	1
7	artificial_mixture	mnm_oracle+flash_residual	836	4	5.50	0.9892249	0.510	0.024	0.2219348	5.00	0.9947853	0.652	0.012	1
8	artificial_mixture	mnm_oracle+oracle_residual	849	3	5.00	0.9917202	0.516	0.031	0.2270694	4.00	0.9966120	0.654	0.016	1
19	gtex_mixture	mnm_shared+flash_residual	727	0	7.00	0.9752919	0.435	0.044	0.1654953	7.00	0.9752919	1.000	0.044	1
20	gtex_mixture	mnm_shared+oracle_residual	791	1	6.00	0.9805313	0.460	0.070	0.1910470	6.00	0.9805313	1.000	0.070	1
11	gtex_mixture	mnm_ed+flash_residual	852	0	5.00	0.9900599	0.513	0.036	0.1773469	4.00	0.9932467	0.722	0.033	1
13	gtex_mixture	mnm_identity+flash_residual	859	0	6.00	0.9852909	0.515	0.044	0.1611565	4.00	0.9941465	0.435	0.025	1
12	gtex_mixture	mnm_ed+oracle_residual	899	0	5.00	0.9920749	0.533	0.049	0.1928185	4.00	0.9954857	0.723	0.046	1
15	gtex_mixture	mnm_naive+flash_residual	946	52	6.00	0.9844498	0.542	0.041	0.3160714	5.00	0.9923752	0.645	0.027	1
14	gtex_mixture	mnm_identity+oracle_residual	927	0	5.50	0.9879113	0.552	0.047	0.1785159	4.00	0.9955277	0.444	0.030	1
16	gtex_mixture	mnm_naive+oracle_residual	991	48	5.50	0.9872693	0.558	0.059	0.3312828	4.00	0.9946095	0.651	0.043	1
17	gtex_mixture	mnm_oracle+flash_residual	1001	0	6.00	0.9855626	0.606	0.032	0.2058061	4.00	0.9925727	0.762	0.031	1
18	gtex_mixture	mnm_oracle+oracle_residual	1034	0	5.00	0.9885851	0.618	0.044	0.2188664	4.00	0.9947450	0.767	0.046	1

With missing data

%cd /home/gaow/GIT/mvarbvs/dsc/mnm_prototype/mnm_missing_20210310

/project2/mstephens/gaow/mvarbvs/dsc/mnm_prototype/mnm_missing_20210310

readRDS("mnm_missing_20210310.cs_summary.rds")$table

	simulate_missing	method	total	overlap_cs	size	purity	power	fdr	cs_correlation	size_cond_cs	purity_cond_cs	power_cond_cs	fdr_cond_cs	converged
9	artificial_mixture_missing	mnm_shared+flash_residual	362	0	7.00	0.9830469	0.221	0.041	0.1650990	7.0	0.9830469	1.000	0.049	1
10	artificial_mixture_missing	mnm_shared+oracle_residual	376	0	7.00	0.9847653	0.229	0.053	0.1663213	7.0	0.9847653	1.000	0.066	1
3	artificial_mixture_missing	mnm_identity+flash_residual	525	0	7.00	0.9846755	0.319	0.046	0.1448854	5.0	0.9901590	0.373	0.043	1
4	artificial_mixture_missing	mnm_identity+oracle_residual	540	0	7.00	0.9841884	0.324	0.056	0.1421742	5.0	0.9912192	0.374	0.052	1
1	artificial_mixture_missing	mnm_ed+flash_residual	566	0	6.50	0.9834907	0.343	0.039	0.1445710	5.0	0.9899533	0.655	0.037	1
5	artificial_mixture_missing	mnm_naive+flash_residual	577	9	7.50	0.9821502	0.346	0.043	0.2127332	6.0	0.9899212	0.546	0.044	1
2	artificial_mixture_missing	mnm_ed+oracle_residual	583	0	6.00	0.9848657	0.350	0.043	0.1452851	5.0	0.9908522	0.641	0.048	1
6	artificial_mixture_missing	mnm_naive+oracle_residual	596	12	7.50	0.9821361	0.357	0.044	0.2234205	5.0	0.9906618	0.542	0.044	1
7	artificial_mixture_missing	mnm_oracle+flash_residual	634	0	7.50	0.9766704	0.392	0.036	0.1727814	6.0	0.9862675	0.648	0.035	1
8	artificial_mixture_missing	mnm_oracle+oracle_residual	640	0	7.00	0.9792363	0.392	0.038	0.1723756	6.0	0.9871464	0.641	0.040	1
13	gtex_mixture_missing	mnm_identity+flash_residual	559	0	8.25	0.9681508	0.340	0.034	0.1433610	7.0	0.9761086	0.295	0.028	1
19	gtex_mixture_missing	mnm_shared+flash_residual	596	1	8.00	0.9635047	0.354	0.054	0.1502047	8.0	0.9635047	1.000	0.054	1
20	gtex_mixture_missing	mnm_shared+oracle_residual	615	1	8.00	0.9654032	0.357	0.073	0.1571954	8.0	0.9654032	1.000	0.073	1
14	gtex_mixture_missing	mnm_identity+oracle_residual	599	0	7.50	0.9705975	0.359	0.047	0.1450632	6.0	0.9795966	0.302	0.031	1
11	gtex_mixture_missing	mnm_ed+flash_residual	607	0	6.00	0.9760011	0.361	0.051	0.1412279	6.0	0.9814829	0.708	0.050	1
12	gtex_mixture_missing	mnm_ed+oracle_residual	634	0	6.00	0.9776738	0.374	0.057	0.1541462	6.0	0.9833429	0.706	0.057	1
15	gtex_mixture_missing	mnm_naive+flash_residual	689	16	8.00	0.9676551	0.405	0.048	0.2195710	6.0	0.9770371	0.651	0.046	1
16	gtex_mixture_missing	mnm_naive+oracle_residual	712	17	7.00	0.9681700	0.412	0.053	0.2276102	6.0	0.9788229	0.650	0.051	1
17	gtex_mixture_missing	mnm_oracle+flash_residual	744	0	7.00	0.9659596	0.448	0.047	0.1714753	6.5	0.9760616	0.750	0.046	1
18	gtex_mixture_missing	mnm_oracle+oracle_residual	767	0	7.00	0.9700133	0.455	0.053	0.1725628	6.0	0.9789470	0.751	0.055	1

PIPs

%cd /home/gaow/GIT/mvarbvs/dsc/mnm_prototype/mnm_20210310

/project2/mstephens/gaow/mvarbvs/dsc/mnm_prototype/mnm_20210310

Calibration (condition specific)

%preview mnm_20210310.artificial_mixture.pip_condition.calibration.png

> mnm_20210310.artificial_mixture.pip_condition.calibration.png (86.4 KiB):

%preview mnm_20210310.gtex_mixture.pip_condition.calibration.png

> mnm_20210310.gtex_mixture.pip_condition.calibration.png (85.6 KiB):

Calibration (global)

%preview mnm_20210310.artificial_mixture.pip_global.calibration.png

> mnm_20210310.artificial_mixture.pip_global.calibration.png (93.0 KiB):

%preview mnm_20210310.gtex_mixture.pip_global.calibration.png

> mnm_20210310.gtex_mixture.pip_global.calibration.png (93.0 KiB):

ROC (condition specific)

%preview mnm_20210310.artificial_mixture.pip_condition.curves.roc.pdf -s png

> mnm_20210310.artificial_mixture.pip_condition.curves.roc.pdf (52.6 KiB):

%preview mnm_20210310.gtex_mixture.pip_condition.curves.roc.pdf -s png

> mnm_20210310.gtex_mixture.pip_condition.curves.roc.pdf (53.0 KiB):

ROC (global)

%preview mnm_20210310.artificial_mixture.pip_global.curves.roc.pdf -s png

> mnm_20210310.artificial_mixture.pip_global.curves.roc.pdf (28.1 KiB):

%preview mnm_20210310.gtex_mixture.pip_global.curves.roc.pdf -s png

> mnm_20210310.gtex_mixture.pip_global.curves.roc.pdf (30.8 KiB):

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Copyright © 2016-2020 Gao Wang et al at Stephens Lab, University of Chicago