In this vignette, we demonstrate a procedure that helps SuSiE get out of local optimum.

We simulate phenotype using UK Biobank genotypes from 50,000 individuals. There are 1001 SNPs. It is simulated to have exactly 2 non-zero effects at 234, 287.

```
library(susieR)
library(curl)
<- tempfile(fileext = ".RData")
data_file <- paste0("https://raw.githubusercontent.com/stephenslab/susieR/",
data_url "master/inst/datafiles/FinemappingConvergence1k.RData")
curl_download(data_url,data_file)
load(data_file)
<- FinemappingConvergence$true_coef
b susie_plot(FinemappingConvergence$z, y = "z", b=b)
```

The strongest marginal association is a non-effect SNP.

Since the sample size is large, we use sufficient statistics (\(X^\intercal X, X^\intercal y, y^\intercal
y\) and sample size \(n\)) to
fit susie model. It identifies 2 Credible Sets, one of them is false
positive. This is because `susieR`

get stuck around a local
minimum.

```
<- with(FinemappingConvergence,
fitted susie_suff_stat(XtX = XtX, Xty = Xty, yty = yty, n = n))
susie_plot(fitted, y="PIP", b=b, main=paste0("ELBO = ", round(susie_get_objective(fitted),2)))
```

Our refine procedure to get out of local optimum is

fit a susie model, \(s\) (suppose it has \(K\) CSs).

for CS in \(s\), set SNPs in CS to have prior weight 0, fit susie model –> we have K susie models: \(t_1, \cdots, t_K\).

for each \(k = 1, \cdots, K\), fit susie with initialization at \(t_k\) (\(\alpha, \mu, \mu^2\)) –> \(s_k\)

if \(\max_k \text{elbo}(s_k) > \text{elbo}(s)\), set \(s = s_{kmax}\) where \(kmax = \arg_k \max \text{elbo}(s_k)\) and go to step 2; if no, break.

We fit susie model with above procedure by setting
`refine = TRUE`

.

```
<- with(FinemappingConvergence,
fitted_refine susie_suff_stat(XtX = XtX, Xty = Xty, yty = yty,
n = n, refine=TRUE))
# WARNING: XtX is not symmetric; forcing XtX to be symmetric by replacing XtX with (XtX + t(XtX))/2
# WARNING: XtX is not symmetric; forcing XtX to be symmetric by replacing XtX with (XtX + t(XtX))/2
# WARNING: XtX is not symmetric; forcing XtX to be symmetric by replacing XtX with (XtX + t(XtX))/2
# WARNING: XtX is not symmetric; forcing XtX to be symmetric by replacing XtX with (XtX + t(XtX))/2
# WARNING: XtX is not symmetric; forcing XtX to be symmetric by replacing XtX with (XtX + t(XtX))/2
# WARNING: XtX is not symmetric; forcing XtX to be symmetric by replacing XtX with (XtX + t(XtX))/2
# WARNING: XtX is not symmetric; forcing XtX to be symmetric by replacing XtX with (XtX + t(XtX))/2
# WARNING: XtX is not symmetric; forcing XtX to be symmetric by replacing XtX with (XtX + t(XtX))/2
# WARNING: XtX is not symmetric; forcing XtX to be symmetric by replacing XtX with (XtX + t(XtX))/2
# WARNING: XtX is not symmetric; forcing XtX to be symmetric by replacing XtX with (XtX + t(XtX))/2
susie_plot(fitted_refine, y="PIP", b=b, main=paste0("ELBO = ", round(susie_get_objective(fitted_refine),2)))
```

With the refine procedure, it identifies 2 CSs with the true signals, and the achieved evidence lower bound (ELBO) is higher.

Here are some details about the computing environment, including the versions of R, and the R packages, used to generate these results.

```
sessionInfo()
# R version 3.6.2 (2019-12-12)
# Platform: x86_64-apple-darwin15.6.0 (64-bit)
# Running under: macOS Catalina 10.15.7
#
# Matrix products: default
# BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
# LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
#
# locale:
# [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#
# attached base packages:
# [1] stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] curl_4.3 Matrix_1.2-18 susieR_0.12.35
#
# loaded via a namespace (and not attached):
# [1] tidyselect_1.1.1 xfun_0.29 bslib_0.3.1 purrr_0.3.4
# [5] lattice_0.20-38 colorspace_1.4-1 vctrs_0.3.8 generics_0.0.2
# [9] htmltools_0.5.2 yaml_2.2.0 utf8_1.1.4 rlang_1.0.6
# [13] mixsqp_0.3-46 jquerylib_0.1.4 pillar_1.6.2 glue_1.4.2
# [17] DBI_1.1.0 RcppZiggurat_0.1.5 matrixStats_0.63.0 lifecycle_1.0.0
# [21] plyr_1.8.5 stringr_1.4.0 munsell_0.5.0 gtable_0.3.0
# [25] evaluate_0.14 knitr_1.37 fastmap_1.1.0 parallel_3.6.2
# [29] irlba_2.3.3 fansi_0.4.0 Rfast_2.0.3 highr_0.8
# [33] Rcpp_1.0.8 scales_1.1.0 jsonlite_1.7.2 ggplot2_3.3.6
# [37] digest_0.6.23 stringi_1.4.3 dplyr_1.0.7 grid_3.6.2
# [41] cli_3.5.0 tools_3.6.2 magrittr_2.0.1 sass_0.4.0
# [45] tibble_3.1.3 crayon_1.4.1 pkgconfig_2.0.3 ellipsis_0.3.2
# [49] assertthat_0.2.1 rmarkdown_2.11 reshape_0.8.8 R6_2.4.1
# [53] compiler_3.6.2
```