SHAJAM: SHA-JAM Fit SHA-JAM
In USCbiostats/hJAM: Hierarchical Joint Analysis of Marginal Summary Statistics

SHAJAM

R Documentation

SHA-JAM Fit SHA-JAM

Description

Function to implement SHA-JAM

Usage

SHAJAM(
  betas.Gy,
  betas_se.Gy = NULL,
  N.Gy,
  eaf.Gy = NULL,
  Geno,
  A,
  L.cs = NULL,
  min_abs_corr = NULL,
  coverage = 0.95,
  estimate_residual_variance = TRUE,
  max_iter = 500
)

Arguments

`betas.Gy`	The betas in the paper: the marginal effects of SNPs on the phenotype (Gy)
`betas_se.Gy`	The standard errors of the betas
`N.Gy`	The sample size of the GWAS where you obtain the betas.Gy and betas_se.Gy
`eaf.Gy`	The reference allele frequency of the SNPs in betas.Gy
`Geno`	The individual level data of the reference panel. Must have the same order of SNPs as in the betas.Gy.
`A`	The conditional A matrix.
`L.cs`	The largest number of credible set allowed in SHA-JAM. Required by SHA-JAM.
`min_abs_corr`	The requested minimum absolute correlation coefficient between intermediates within one credible set. Required by SHA-JAM.
`coverage`	The coverage of credible set. Default is 0.95. Required by SHA-JAM.
`estimate_residual_variance`	If estimate the residual variance in the fitting procedure of SHA-JAM. Default as TRUE. Required by SHA-JAM.
`max_iter`	The number of maximum iterations in fitting SHA-JAM. Required by SHA-JAM.

Value

An object of the SHAJAM

numSNP: The number of SNPs used in the analysis.
numX: The number of intermediates in the analysis.
Selected_variable_length: The number of selected intermediates, regardless of the credible sets.
Selected_variable_name: The label/name for each selected intermediates.
Coefficients: The coefficients of selected intermediates.
Selected_variable_pip: The posterior inclusion probability of each selected intermediate.
num_Credible_sets: Number of credible sets.
all_variables: The label/name for all candidate intermediates.
all_variable_pip: The posterior inclusion probability of all candidate intermediates.
all_variable_coefficient: The coefficients of all candidate intermediates.
cs_purity: The purity of the credibel set selected.