GWAS for latent factors at one variant using observed trait GWAS summary statistics

latentGWAS(
  obsGWAS,
  covY,
  L,
  beta_colname = "BETA",
  se_colname = "SE",
  snpID_colname = "SNP",
  EAF
)

Arguments

obsGWAS: list of observed GWAS data.frames, containing the effect estimates and standard errors and snp names, at a minimum
covY: trait covariance matrix (same as used in factor analysis)
L: PxK matrix of factor loadings generated from a factor analysis of P observed traits and K latent factors (K<P)
beta_colname: text column name for the effect estimates in each obsGWAS data.frame; default "BETA"
se_colname: text column name for the effect estimate standard errors in each obsGWAS data.frame; default "SE"
snpID_colname: text column name for the effect estimates in each obsGWAS data.frame; default "SNP"
EAF: vector of effect allele frequencies in same order as variants in obsGWAS

list of latent GWAS results in format for flashfmZero, with columns rsID, beta, EAF, beta_se, p-value

Jenn Asimit