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?