s_hat_bigsnp: Step Two of bigsnp2mashr

In Alice-MacQueen/CDBNgenomics: Genomics Using the Cooperative Dry Bean Nursery Dataset

Description

Step Two of bigsnp2mashr

Usage

s_hat_bigsnp(
  path,
  gwas_rds,
  phenotype,
  top_set,
  random_sample,
  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
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?

Alice-MacQueen/CDBNgenomics documentation built on Aug. 18, 2020, 4:39 p.m.