PMR_individual: PPMR Individual-level Analysis

In PPMR: Probabilistic Two Sample Mendelian Randomization

PPMR Individual-level Analysis

Description

PPMR Individual-level Analysis

Usage

PMR_individual(yin, zin, x1in, x2in, gammain, alphain, max_iterin, epsin)

Arguments

yin	Numeric vector of the outcome variable (length n1).
zin	Numeric vector of the mediator variable (length n2).
x1in	Numeric n1 \times p matrix of SNP genotypes for the outcome model.
x2in	Numeric n2 \times p matrix of SNP genotypes for the mediator model. Must have the same number of columns p as x1in.
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 of the outcome model.
sigmaY	Residual variance of the mediator 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 before convergence.

Examples

# ---- Simulate simple example data ----
set.seed(456)
n1 <- 8
n2 <- 10
p  <- 3

# Outcome and mediator vectors
y <- c(0.5, -0.3, 0.1, 0.4, -0.2, 0.0, 0.6, -0.1)
z <- c(0.2, -0.4, 0.3, 0.1, -0.1, 0.5, 0.0, 0.4, -0.3, 0.2)

# Fixed genotype design matrices (n × p) with mild correlations
x1 <- matrix(c(
  1.0, 0.2, 0.1,
  0.2, 1.0, 0.3,
  0.1, 0.3, 1.0,
  0.4, 0.1, 0.2,
  0.2, 0.4, 0.3,
  0.3, 0.2, 0.4,
  0.5, 0.1, 0.3,
  0.1, 0.5, 0.2
), nrow = n1, byrow = TRUE)

x2 <- matrix(c(
  1.0, 0.3, 0.2,
  0.3, 1.0, 0.4,
  0.2, 0.4, 1.0,
  0.5, 0.1, 0.3,
  0.2, 0.5, 0.1,
  0.3, 0.2, 0.4,
  0.4, 0.3, 0.2,
  0.1, 0.4, 0.3,
  0.2, 0.1, 0.5,
  0.3, 0.2, 0.4
), nrow = n2, byrow = TRUE)

# Run PPMR individual-level analysis
PMR_individual(
  yin        = y,
  zin        = z,
  x1in       = x1,
  x2in       = x2,
  gammain    = 0,
  alphain    = 0,
  max_iterin = 50,
  epsin      = 1e-6
)

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