mcnemar permutation test — mcnemar_test_permut.result_snps • gwid

mcnemar permutation test

Usage

# S3 method for class 'result_snps'
mcnemar_test_permut(
  mcnemar = "object of class result_snps (output of function mcnemar_test with fun=sum)",
  roh_mat = "output of roh function when roh_mat = TRUE",
  gwas = "object of class gwas",
  nperm = 1000,
  reference = "cases",
  w,
  ...
)

Arguments

mcnemar: macnemar test output
roh_mat: roh matrix
gwas: gwas
nperm: number of permutation
reference: reference group
w: window
...: other variables

Value

the output will be a test_snps (data.table) object including 3 columns: “snp_pos”, “case_control”, and “value” which is a p-values.