Step Two of bigsnp2mashr

s_hat_bigsnp(
  path,
  gwas_rds,
  phenotype,
  top_set,
  random_sample,
  scaled = TRUE,
  markers = NULL,
  markers2 = NULL,
  model = c("linear", "logistic"),
  clump = TRUE
)

Arguments

path: Path
gwas_rds: RDS file with gwas results
phenotype: Character vector. Single phenotype name
top_set: Top markers chosen
random_sample: Numeric vector. Random sample of SNPs
scaled: Logical. Should effect sizes and std errors be scaled?
markers: Marker names for the GWAS you ran
markers2: Markers to include if SNPs are LD clumped.
model: One of linear or logistic. Type of GWAS model.
clump: Logical. Clump SNPs?