susieJAM_A: Compute conditional A using SuSiE JAM

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

Compute conditional A using SuSiE JAM

Description

The susieJAM_A function is to get the conditional A matrix by using marginal A matrix

Usage

susieJAM_A(
  marginalA,
  marginalA_se,
  N.Gx,
  eaf.Gy = NULL,
  Geno,
  inclusion.indicator,
  L.cs,
  min_abs_corr,
  max_iter,
  coverage,
  estimate_residual_variance = TRUE
)

Arguments

marginalA	the marginal effects of SNPs on the exposures (Gx).
marginalA_se	the standard error of the marginal effects of SNPs on the exposures (Gx).
N.Gx	the sample size of each Gx. It can be a scalar or a vector. If there are multiple X's from different Gx, it should be a vector including the sample size of each Gx. If all alphas are from the same Gx, it could be a scalar.
eaf.Gy	the effect allele frequency of the SNPs in the Gx data.
Geno	the reference panel (Geno), such as 1000 Genome。
inclusion.indicator	The matrix of inclusion indicator of SNPs for each intermediate. Included as 1; otherwise 0.
L.cs	A susie input parameter. Number of components (nonzero elements) in the SuSiE regression model. If L.cs is larger than the number of covariate (p), L.cs is set to p.
min_abs_corr	A susie input parameter. Minimum of absolute value of correlation allowed in a credible set. The default, 0.5, corresponds to squared correlation of 0.25, which is a commonly used threshold for genotype data in genetics studies.
max_iter	Maximum number of iterations in SuSiE fitting.
coverage	Default as 0.95.The coveralge level of the credible set.
estimate_residual_variance	Default as TRUE. Estimate the residual variance in each iteration of SuSiE fitting.

Value

A matrix with conditional estimates which are converted from marginal estimates using the susie JAM model.

Author(s)

Lai Jiang

Examples

data(GTEx.PrCa)
susieJAM_A(marginalA = GTEx.PrCa.marginal.A[, 1:9],
marginalA_se = GTEx.PrCa.marginal.A.se[, 1:9], eaf.Gy = GTEx.PrCa.maf.gwas,
Geno = GTEx.PrCa.Geno, inclusion.indicator = GTEx.PrCa.inclusion.indicator,
N.Gx = 620, L.cs = 10, min_abs_corr = 0.5)

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