mJAM_get_condp_selected: Get conditional p-value for selected (index SNPs) under mJAM...

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

Get conditional p-value for selected (index SNPs) under mJAM model

Description

Get conditional p-value for selected (index SNPs) under mJAM model

Usage

mJAM_get_condp_selected(
  GItGI,
  GIty,
  yty,
  yty_med,
  N_GWAS,
  g = NULL,
  selected_id,
  use_robust_var_est = FALSE,
  use_median_yty_ethnic = NULL,
  rare_SNPs = NULL
)

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.
g	Hyperparameter in g-prior. If 'NULL', it will be set to 'sum(N_GWAS)'.
selected_id	A numeric vector of IDs of previously selected index SNP(s).
use_robust_var_est	whether to use linear combination of median yty and individual yty. (only for mJAM-Forward)
use_median_yty_ethnic	A numeric vector of study index in which median_yty is used for all SNPs in 'selected_id'.
rare_SNPs	A character vector for rare SNP(s) which we do not apply weighting. Instead, we use the individual estimate of yty for these SNPs for robustness.

Value

b_joint

The estimated conditional effect size when all SNPs in 'selected_id' are in one mJAM model.

b_joint_var

The variance of 'b_joint'.

condp

A vector of all conditional p-values for 'b_joint'.

Author(s)

Jiayi Shen

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