Simultaneous analysis of genetic associations with multiple phenotypes may reveal shared genetic susceptibility across traits (pleiotropy). CPBayes is a Bayesian meta analysis method for studying cross-phenotype genetic associations. It uses summary-level data across multiple phenotypes to simultaneously measure the evidence of aggregate-level pleiotropic association and estimate an optimal subset of traits associated with the risk locus. CPBayes model is based on a spike and slab prior.

This R-package consists of following functions:

- analytic_locFDR_BF_uncor: This function analytically computes the local FDR & Bayes factor (BF) that quantifies the evidence of aggregate-level pleiotropic association for uncorrelated summary statistics.
- cpbayes_uncor: It implements CPBayes for uncorrelated summary statistics to figure out the optimal subset of non-null traits underlying a pleiotropic signal and other insights. The summary statistics across traits/studies are uncorrelated when the studies have no overlapping and genetically related subjects.
- analytic_locFDR_BF_cor: This function analytically computes the local FDR & Bayes factor (BF) that quantifies the evidence of aggregate-level pleiotropic association for correlated summary statistics.
- cpbayes_cor: It implements CPBayes for correlated summary statistics to figure out the optimal subset of non-null traits underlying a pleiotropic signal and other insights. The summary statistics across traits/studies are correlated when the studies have overlapping/genetically related subjects or the phenotypes were measured in a cohort study.
- post_summaries: It summarizes the MCMC data produced by cpbayes_uncor or cpbayes_cor. It computes additional summaries to provide a better insight into a pleiotropic signal. It works in the same way for both cpbayes_uncor and cpbayes_cor.
- forest_cpbayes: It creates a forest plot presenting the pleiotropy result obtained by cpbayes_uncor or cpbayes_cor. It works in the same way for both cpbayes_uncor and cpbayes_cor.
- estimate_corln: It computes an approximate correlation matrix of the beta-hat vector for multiple overlapping case-control studies using the sample-overlap count matrices.

You can install CPBayes from CRAN.

```
install.packages("CPBayes")
library("CPBayes")
```

Get the path to the data.

```
library("CPBayes")
# Load the beta hat vector
<- system.file("extdata", "BetaHat.rda", package = "CPBayes")
BetaHatfile load(BetaHatfile)
BetaHat
```

BetaHat contains an example data of the main genetic effect (beta/log(odds ratio)) estimates for a single nucleotide polymorphism (SNP) obtained from 10 separate case-control studies for 10 different diseases. Since the studies do not have any overlapping subject, beta-hat across the diseases can be assumed uncorrelated.

```
# Load the standard error vector
<- system.file("extdata", "SE.rda", package = "CPBayes")
SEfile load(SEfile)
SE
```

SE contains the standard errors corresponding to the above beta hat vector across 10 separate case-control studies.

Next we specify the name of the diseases/phenotypes and the genetic variant.

```
# Specify the name of the traits and the genetic variant.
<- paste("Disease", 1:10, sep = "")
traitNames <- "rs1234"
SNP1
traitNames SNP1
```

Now, since the studies are non-overlapping, the summary statistics across traits are uncorrelated. Here we run the analytic_locFDR_BF_uncor function for this example data.

```
#Run analytic_locFDR_BF_uncor function to analytically compute locFDR and log10BF for uncorrelated summary statistics.
<- analytic_locFDR_BF_uncor(BetaHat, SE)
result str(result)
```

This function provides analytically computed locFDR [result\(locFDR\] and log10(Bayes factor) \[result\)log10_BF] for uncorrelated summary statistics. While analytically computing locFDR (BF), a fixed value of slab variance is considered.

Now we implement CPBayes (based on MCMC) for this example data. Since the studies are non-overlapping, we run the the cpbayes_uncor function.

```
# Run the uncorrelated version of CPBayes.
<- cpbayes_uncor(BetaHat, SE, Phenotypes = traitNames, Variant = SNP1) result
```

After running cpbayes_uncor, it prints the list of important traits for which the trait-specific posterior probability of association (PPAj) > 20%. However, the printed outputs are only a part of ‘result’ which is a list that constitutes of various components. An overall summary of ‘result’ can be seen by using the str() function (as shown below).

```
# Overall summary of the primary results produced by cpbayes_uncor.
str(result)
```

A detailed interpretation of all the outputs are described in the Value section of cpbayes_uncor in the CPBayes manual.

The post_summaries function provides important insights into an observed pleiotropic signal, e.g., the direction of associations, trait-specific posterior probability of associations (PPAj), posterior mean/median and 95% credible interval (Bayesian analog of the confidence interval) of the unknown true genetic effect (beta/odds ratio) on each trait, etc.

```
# Post summary of the MCMC data produced by cpbayes_uncor.
<- post_summaries(result, level = 0.05)
PleioSumm str(PleioSumm)
```

So we have to pass the list ‘result’ returned by cpbayes_uncor as the first argument and the ‘level’ as the second argument into the post_summaries function. If ‘level’ is not specified, the default value is 0.05. For detailed description of different outputs provided by this function, see the Value section of post_summaries in the CPBayes manual.

Next we run the forest_cpbayes function to create a forest plot that presents the pleiotropy result produced by cpbayes_uncor.

```
# Forest plot for the pleiotropy result obtained by cpbayes_uncor.
forest_cpbayes(result, level = 0.05)
```

Similarly as for the post_summaries function, we need to pass the same list `result’ returned by cpbayes_uncor as the first argument into the function. Second argument is the level whose default value is 0.05. In the forest plot, (1-level)% confidence interval of the beta/log odds ratio parameter is plotted for each trait. For more details, see the section of forest_cpbayes function in the CPBayes manual.

Next we demonstrate how to run CPBayes for correlated summary statistics. Get the path to the data.

```
# Load the beta-hat vector
<- system.file("extdata", "cBetaHat.rda", package = "CPBayes")
datafile load(datafile)
cBetaHat
```

Here ‘c’ in cBetaHat stands for correlated case. cBetaHat contains an example data of the main genetic association parameter (beta/log odds ratio) estimates for a SNP across 10 overlapping case-control studies for 10 different diseases. Each of the 10 studies has a distinct set of 7000 cases and a common set of 10000 controls shared across all the studies. Since the studies have overlapping subjects, beta-hat across the diseases are correlated.

```
# Load the standard error vector
<- system.file("extdata", "cSE.rda", package = "CPBayes")
datafile load(datafile)
cSE
```

cSE contains the standard errors corresponding to the above beta hat vector across 10 overlapping case-control studies.

```
# Load the correlation matrix of the beta-hat vector (cBetaHat)
<- system.file("extdata", "cor.rda", package = "CPBayes")
datafile load(datafile)
cor
```

The correlation matrix of the beta-hat vector (cBetaHat) is given by ‘cor’ which we estimated by employing the estimate_corln function (demonstrated later in this tutorial) using the sample-overlap matrices (explained later in this tutorial).

Since the summary statistics across traits are correlated, we run the the analytic_locFDR_BF_cor function for this example data.

```
# Run analytic_locFDR_BF_cor function to analytically compute locFDR and log10BF for correlated summary statistics.
<- analytic_locFDR_BF_cor(cBetaHat, cSE, cor)
result str(result)
```

So this function analytically computes the locFDR [result\(locFDR\] and log10(Bayes factor) \[result\)log10_BF] for correlated summary statistics. Next we run the correlated version of CPBayes (based on MCMC) for this example data.

```
# Run the correlated version of CPBayes.
<- cpbayes_cor(cBetaHat, cSE, cor, Phenotypes = traitNames, Variant = SNP1) result
```

After running cpbayes_cor, it prints the list of important traits for which the trait-specific posterior probability of association (PPAj) > 20%. However, the printed outputs are only a part of ‘result’ which is a list that constitutes of various components. An overall summary of ‘result’ can be seen by using the str() function (as shown below).

```
# Overall summary of the primary results produced by cpbayes_cor.
str(result)
```

A detailed interpretation of all the outputs are described in the Value section of cpbayes_cor in the CPBayes manual.

The post_summaries function provides important insights into an observed pleiotropic signal, e.g., the direction of associations, trait-specific posterior probability of associations (PPAj), posterior mean/median and 95% credible interval (Bayesian analog of the confidence interval) of the unknown true genetic effect (beta/odds ratio) on each trait, etc.

```
# Post summary of the MCMC data produced by cpbayes_cor.
<- post_summaries(result, level = 0.05)
PleioSumm str(PleioSumm)
```

post_summaries works exactly in the same way for both cpbayes_cor and cpbayes_uncor. For detailed description of different outputs provided by post_summaries, see the Value section of post_summaries in the CPBayes manual.

Next we run the forest_cpbayes function to create a forest plot that presents the pleiotropy result produced by cpbayes_cor.

```
# Forest plot for the pleiotropy result obtained by cpbayes_cor.
forest_cpbayes(result, level = 0.05)
```

Note that, forest_cpbayes works exactly in the same way for both cpbayes_cor and cpbayes_uncor. For more details, see the section of forest_cpbayes function in the CPBayes manual.

The function estimate_corln estimates the correlation matrix of the beta-hat vector for multiple overlapping case-control studies using the sample-overlap count matrices which describe the number of cases or controls shared between studies/traits, and the number of subjects who are case for one study/trait but control for another study/trait. For a cohort study, the phenotypic correlation matrix should be a reasonable substitute of this correlation matrix.

```
# Example data of sample-overlap matrices
<- system.file("extdata", "SampleOverlapMatrix.rda", package = "CPBayes")
SampleOverlapMatrixFile load(SampleOverlapMatrixFile)
SampleOverlapMatrix
```

SampleOverlapMatrix is a list that contains an example of the sample overlap matrices for five different diseases in the Kaiser GERA cohort (a real data). The list constitutes of three matrices as follows. SampleOverlapMatrix\(n11 provides the number of cases shared between all possible pairs of studies/traits. SampleOverlapMatrix\)n00 provides the number of controls shared between all possible pairs of studies/traits. SampleOverlapMatrix$n10 provides the number of subjects who are case for one study/trait and control for another study/trait. For more detailed explanation, see the Arguments section of estimate_corln in the CPBayes manual.

```
# Estimate the correlation matrix of correlated beta-hat vector
<- SampleOverlapMatrix$n11
n11 <- SampleOverlapMatrix$n00
n00 <- SampleOverlapMatrix$n10
n10 <- estimate_corln(n11, n00, n10)
cor cor
```

The function estimate_corln computes an approximate correlation matrix of the correlated beta-hat vector obtained from multiple overlapping case-control studies using the sample-overlap matrices. Note that for a cohort study, the phenotypic correlation matrix should be a reasonable substitute of this correlation matrix. These approximations of the correlation structure are accurate when none of the diseases/traits is associated with the environmental covariates and genetic variant. While demonstrating cpbayes_cor, we used simulated data for 10 overlapping case-control studies with each study having a distinct set of 7000 cases and a common set of 10000 controls shared across all the studies. We used the estimate_corln function to estimate the correlation matrix of the correlated beta-hat vector using the sample-overlap matrices.

** Important note on the estimation of correlation structure
of correlated beta-hat vector:** In general, environmental
covariates are expected to be present in a study and associated with the
phenotypes of interest. Also, a small proportion of genome-wide genetic
variants are expected to be associated. Hence the above approximations
of the correlation matrix may not be accurate. So in general, we
recommend an alternative strategy to estimate the correlation matrix
using the genome-wide summary statistics data across traits as follows.
First, extract all the SNPs for each of which the trait-specific
univariate association p-value across all the traits are > 0.1. The
trait-specific univariate association p-values are obtained using the
beta-hat and standard error for each trait. Each of the SNPs selected in
this way is either weakly or not associated with any of the phenotypes
(null SNP). Next, select a set of independent null SNPs from the initial
set of null SNPs by using a threshold of r^2 < 0.01 (r: the
correlation between the genotypes at a pair of SNPs). In the absence of
in-sample linkage disequilibrium (LD) information, one can use the
reference panel LD information for this screening. Finally, compute the
correlation matrix of the effect estimates (beta-hat vector) as the
sample correlation matrix of the beta-hat vector across all the selected
independent null SNPs. This strategy is more general and applicable to a
cohort study or multiple overlapping studies for binary or quantitative
traits with arbitrary distributions. It is also useful when the beta-hat
vector for multiple non-overlapping studies become correlated due to
genetically related individuals across studies. Misspecification of the
correlation structure can affect the results produced by CPBayes to some
extent. Hence, if genome-wide summary statistics data across traits is
available, we recommend this alternative strategy to estimate the
correlation matrix of the beta-hat vector.

Please see the vignettes (tutorial) and the manual of CPBayes for more detailed description about the package. If you encounter any problem/issue related to the package, please email to statgen.arunabha@gmail.com and tanushree.haldar@gmail.com. Also, see our paper for more details: Majumdar A, Haldar T, Bhattacharya S, Witte JS (2018) An efficient Bayesian meta analysis approach for studying cross-phenotype genetic associations. PLoS Genet 14(2): e1007139.