PMR_summary: PPMR Summary-level Analysis

In PPMR: Probabilistic Two Sample Mendelian Randomization

PPMR Summary-level Analysis

Description

PPMR Summary-level Analysis

Usage

PMR_summary(
  betaxin,
  betayin,
  Sigma1sin,
  Sigma2sin,
  samplen1,
  samplen2,
  gammain,
  alphain,
  max_iterin,
  epsin
)

Arguments

betaxin	Numeric vector of estimated SNP–exposure effects (length 'p').
betayin	Numeric vector of estimated SNP–outcome effects (length 'p').
Sigma1sin	Numeric 'p x p' covariance matrix for the exposure SNP associations (typically an LD matrix).
Sigma2sin	Numeric 'p x p' covariance matrix for the outcome SNP associations.
samplen1	Integer. Sample size used to estimate betaxin.
samplen2	Integer. Sample size used to estimate betayin.
gammain	Integer flag (0/1). If 1, constrains the gamma parameter to 0.
alphain	Integer flag (0/1). If 1, constrains the alpha parameter to 0.
max_iterin	Integer. Maximum number of EM iterations (default: 50 or more).
epsin	Numeric. Convergence tolerance for the log-likelihood.

Value

A named list with elements:

alpha	Estimated causal effect of the mediator on the outcome.
gamma	Estimated direct effect of the SNPs on the outcome.
sigmaX	Residual variance for the exposure model.
sigmaY	Residual variance for the outcome model.
sigmabeta	Variance of the genetic effects.
loglik_seq	Vector of log-likelihood values across iterations.
loglik	Final log-likelihood value.
iteration	Number of iterations used before convergence.

Examples

# ---- Simulate simple example data ----
set.seed(123)
p  <- 3
n1 <- 10
n2 <- 12
betax <- c(0.2, -0.1, 0.3)
betay <- c(0.1,  0.0, 0.2)
Sigma1 <- matrix(c(0.6, 0.2, 0.1,
                   0.2, 0.5, 0.1,
                   0.1, 0.1, 0.4), 3, 3)
Sigma2 <- matrix(c(0.5, 0.1, 0.0,
                   0.1, 0.6, 0.1,
                   0.0, 0.1, 0.5), 3, 3)

PMR_summary(
  betaxin   = betax,
  betayin   = betay,
  Sigma1sin = Sigma1,
  Sigma2sin = Sigma2,
  samplen1  = n1,
  samplen2  = n2,
  gammain   = 0,
  alphain   = 0,
  max_iterin = 50,
  epsin      = 1e-6
)

PPMR documentation built on Nov. 5, 2025, 5:07 p.m.