This vignette demonstrates how to use `susieR`

with
“summary statistics” in the context of genetic fine-mapping. We use the
same simulated data as in fine mapping
vignette. The simulated data are expression levels of a gene (\(y\)) in \(N
\approx 600\) individuals. We want to identify with the genotype
matrix \(X_{N\times P}\) (\(P=1001\)) the genetic variables that causes
changes in expression level. This data set is shipped with
`susieR`

. It is simulated to have exactly three non-zero
effects.

```
library(susieR)
# Warning: replacing previous import 'lifecycle::last_warnings' by
# 'rlang::last_warnings' when loading 'tibble'
# Warning: replacing previous import 'lifecycle::last_warnings' by
# 'rlang::last_warnings' when loading 'pillar'
set.seed(1)
```

```
data(N3finemapping)
attach(N3finemapping)
= nrow(X) n
```

Notice that we’ve simulated two sets of \(Y\) as two simulation replicates. Here we’ll focus on the first data-set.

```
dim(Y)
# [1] 574 2
```

Here are the three true signals in the first data-set:

```
<- true_coef[,1]
b plot(b, pch=16, ylab='effect size')
```

```
which(b != 0)
# [1] 403 653 773
```

So the underlying causal variables are 403, 653 and 773.

Summary statistics of genetic association studies typically contain
effect sizes (\(\hat{\beta}\)
coefficient from regression) and p-values. These statisticscan be used
to perform fine-mapping with given an additional input of correlation
matrix between variables. The correlation matrix in genetics is
typically referred to as an “LD matrix” (LD is short for linkage
disequilibrium). One may use external reference panels to estimate it
when this matrix cannot be obtained from samples directly.
*Importantly, the LD matrix has to be a matrix containing estimates
of the correlation, \(r\), and not
\(r^2\) or \(|r|\).* See also this vignette for how to check the
consistency of the LD matrix with the summary statistics.

The `univariate_regression`

function can be used to
compute summary statistics by fitting univariate simple regression
variable by variable. The results are \(\hat{\beta}\) and \(SE(\hat{\beta})\) from which z-scores can
be derived. Alternatively, you can obtain z-scores from \(\hat{\beta}\) and p-values if you are
provided with those information. For example,

```
<- univariate_regression(X, Y[,1])
sumstats <- sumstats$betahat / sumstats$sebetahat
z_scores susie_plot(z_scores, y = "z", b=b)
```

For this example, the correlation matrix can be computed directly from data provided:

`<- cor(X) R `

`susieR`

using summary statisticsBy default, SuSiE assumes at most 10 causal variables, with
`L = 10`

, although we note that SuSiE is generally robust to
the choice of `L`

.

Since the individual-level data is available for us here, we can
easily compute the “in-sample LD” matrix, as well as the variance of
\(y\), which is 7.8424. (By
“in-sample”, we means the LD was computed from the exact same matrix
`X`

that was used to obtain the other statistics.) When we
fit SuSiE regression with summary statistics, \(\hat{\beta}\), \(SE(\hat{\beta})\), \(R\), \(n\), and var_y these are also the
*sufficient statistics.* With an in-sample LD, we can also
estimate the residual variance using these sufficient statistics. (Note
that if the covariate effects are removed from the genotypes in the
univariate regression, it is recommended that the “in-sample” LD matrix
also be computed from the genotypes after the covariate effects have
been removed.)

```
<- susie_rss(bhat = sumstats$betahat, shat = sumstats$sebetahat, n = n, R = R, var_y = var(Y[,1]), L = 10,
fitted_rss1 estimate_residual_variance = TRUE)
# HINT: For estimate_residual_variance = TRUE, please check that R is the "in-sample" LD matrix; that is, the correlation matrix obtained using the exact same data matrix X that was used for the other summary statistics. Also note, when covariates are included in the univariate regressions that produced the summary statistics, also consider removing these effects from X before computing R.
```

Using `summary`

, we can examine the posterior inclusion
probability (PIP) for each variable, and the 95% credible sets:

```
summary(fitted_rss1)$cs
# cs cs_log10bf cs_avg_r2 cs_min_r2
# 1 2 4.033879 1.0000000 1.0000000
# 2 1 6.744086 0.9634847 0.9634847
# 3 3 3.461470 0.9293299 0.7545197
# variable
# 1 653
# 2 773,777
# 3 362,365,372,373,374,379,381,383,384,386,387,388,389,391,392,396,397,398,399,400,401,403,404,405,407,408,415
```

The three causal signals have been captured by the three CSs. Note the third CS contains many variables, including the true causal variable 403.

We can also plot the posterior inclusion probabilities (PIPs):

`susie_plot(fitted_rss1, y="PIP", b=b)`

The true causal variables are shown in red. The 95% CSs are shown by three different colours (green, purple, blue).

Note this result is *exactly the same* as running
`susie`

on the original individual-level data:

```
= susie(X, Y[,1], L = 10)
fitted all.equal(fitted$pip, fitted_rss1$pip)
# [1] TRUE
all.equal(coef(fitted)[-1], coef(fitted_rss1)[-1])
# [1] TRUE
```

If, on the other hand, the variance of \(y\) is unknown, we fit can SuSiE regression
with summary statistics, \(\hat{\beta}\), \(SE(\hat{\beta})\), \(R\) and \(n\) (or *z*-scores, \(R\) and \(n\)). The outputted effect estimates are
now on the standardized \(X\) and \(y\) scale. Still, we can estimate the
residual variance because we have the in-sample LD matrix:

```
= susie_rss(z = z_scores, R = R, n = n, L = 10,
fitted_rss2 estimate_residual_variance = TRUE)
# HINT: For estimate_residual_variance = TRUE, please check that R is the "in-sample" LD matrix; that is, the correlation matrix obtained using the exact same data matrix X that was used for the other summary statistics. Also note, when covariates are included in the univariate regressions that produced the summary statistics, also consider removing these effects from X before computing R.
```

The result is same as if we had run `susie`

on the
individual-level data, but the output effect estimates are on different
scale:

```
all.equal(fitted$pip, fitted_rss2$pip)
# [1] TRUE
plot(coef(fitted)[-1], coef(fitted_rss2)[-1], xlab = 'effects from SuSiE', ylab = 'effects from SuSiE-RSS', xlim=c(-1,1), ylim=c(-0.3,0.3))
```

Specifically, without the variance of \(y\), these estimates are same as if we had applied SuSiE to a standardized \(X\) and \(y\); that is, as if \(y\) and the columns of \(X\) had been normalized so that \(y\) and each column of \(X\) had a standard deviation of 1.

```
= susie(scale(X), scale(Y[,1]), L = 10)
fitted_standardize all.equal(coef(fitted_standardize)[-1], coef(fitted_rss2)[-1])
# [1] TRUE
```

`susieR`

using LD matrix from reference
panelWhen the original genotypes are not available, one may use a separate reference panel to estimate the LD matrix.

To illustrate this, we randomly generated 500 samples from \(N(0,R)\) and treated them as reference
panel genotype matrix `X_ref`

.

We fit the SuSiE regression using out-of sample LD matrix. The residual variance is fixed at 1 because estimating residual variance sometimes produces very inaccurate estimates with out-of-sample LD matrix. The output effect estimates are on the standardized \(X\) and \(y\) scale.

`<- susie_rss(z_scores, R_ref, n=n, L = 10) fitted_rss3 `

`susie_plot(fitted_rss3, y="PIP", b=b)`

In this particular example, the SuSiE result with out-of-sample LD is very similar to using the in-sample LD matrix because the LD matrices are quite similar.

`plot(fitted_rss1$pip, fitted_rss3$pip, ylim=c(0,1), xlab='SuSiE PIP', ylab='SuSiE-RSS PIP')`

In some rare cases, the sample size \(n\) is unknown. When the sample size is not
provided as input to `susie_rss`

, this is in effect assuming
the sample size is infinity and all the effects are small, and the
estimated PVE for each variant will be close to zero. The outputted
effect estimates are on the “noncentrality parameter” scale.

```
= susie_rss(z_scores, R_ref, L = 10)
fitted_rss4 # WARNING: Providing the sample size (n), or even a rough estimate of n, is highly recommended. Without n, the implicit assumption is n is large (Inf) and the effect sizes are small (close to zero).
susie_plot(fitted_rss4, y="PIP", b=b)
```

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] 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] Matrix_1.2-18 assertthat_0.2.1 rmarkdown_2.11 reshape_0.8.8
# [53] R6_2.4.1 compiler_3.6.2
```