mJAM_get_PrM_Wald: Get Pr(Model) based on Wald-type model probability

In USCbiostats/hJAM: Hierarchical Joint Analysis of Marginal Summary Statistics

Get Pr(Model) based on Wald-type model probability

Description

Also apply weighting to get robust estimates of yty

Usage

mJAM_get_PrM_Wald(
  GItGI,
  GIty,
  yty,
  yty_med,
  N_GWAS,
  C_id,
  prev_X_list = NULL,
  g = NULL,
  rare_SNPs = NULL,
  use_robust_var_est = FALSE
)

Arguments

GItGI	A list of transformed statistics from 'get_XtX()' for each study.
GIty	A list of transformed statistics from 'get_z()' for each study.
yty	A list of transformed statistics from 'get_yty()' for each study.
yty_med	A numeric vector of median yty across all SNPs within each study.
N_GWAS	A numeric vector of GWAS sample size for each study.
C_id	An ingeter vector of IDs for the SNPs to be tested.
prev_X_list	A numeric vector of the ID(s) of previously selected index SNP(s).
g	The pre-specified 'g' in 'g'-prior formulation.
rare_SNPs	A numeric vector of ID(s) for rare SNP(s) which we do not apply weighting. Instead, we use the individual estimate of yty for these SNPs for robustness.
use_robust_var_est	whether to use linear combination of median yty and individual yty.

Value

A numeric vector of posterior Pr(Model) for each SNPs in 'C_id'.

Author(s)

Jiayi Shen

USCbiostats/hJAM documentation built on Jan. 26, 2024, 5:27 p.m.