summaryHS: Summary function of Hierarchical Spike

In GCPBayes: Bayesian Meta-Analysis of Pleiotropic Effects Using Group Structure

Summary function of Hierarchical Spike

Description

The summaryHS function serves as a versatile tool for generating result summaries derived from the output of the HS function.

Usage

summaryHS(object)

Arguments

object

a result of a call to HS

Value

• Name of Gene: the component from object.

• Number of SNPs: the component from object.

• Name of SNPs: the component from object.

• Pleiotropic effect based on CI: the component from object.

• Pleiotropic effect based on median thresholding: the component from object.

Author(s)

Taban Baghfalaki.

References

Baghfalaki, T., Sugier, P. E., Truong, T., Pettitt, A. N., Mengersen, K., & Liquet, B. (2021). Bayesian meta analysis models for cross cancer genomic investigation of pleiotropic effects using group structure. Statistics in Medicine, 40(6), 1498-1518.

Examples

# PARP2_summary
data(PARP2_summary)
Breast <- PARP2_summary$Breast
Thyroid <- PARP2_summary$Thyroid
Betah <- list(Breast$beta, Thyroid$beta)
Sigmah <- list(diag(Breast$se), diag(Thyroid$se))
genename <- "PARP2"
snpnames <- Breast$snp
K <- 2
m <- 6

set.seed(123)
RES <- HS(Betah, Sigmah,
  kappa0 = 0.5, kappastar0 = 0.5, sigma20 = 1, s20 = 1,
  m = m, K = K, niter = 800, burnin = 400, nthin = 1, nchains = 1,
  a1 = 0.1, a2 = 0.1, d1 = 0.1, d2 = 0.1, c1 = 1, c2 = 1, e2 = 1, snpnames, genename
)
summaryHS(RES)

GCPBayes documentation built on Nov. 29, 2025, 1:06 a.m.