Make SNP groups using fine-mapping information from all of the traits

Make SNP groups using fine-mapping information from all of the traits

makeSNPgroups(
  main.input,
  is.snpmat,
  min.mppi = 0.01,
  minsnpmppi = 0.01,
  r2.minmerge = 0.5
)

Arguments

main.input

output from flashfm.input function

is.snpmat

logical taking value TRUE when genotype matrix is provided and FALSE when covariance matrix is given

min.mppi

trim snp groups with total MPPI < min.mppi in all diseases; default 0.01

minsnpmppi

min snp mppi

r2.minmerge

merge groups with minimum between-group r2 > r2.minmerge; default 0.5

Value

list of SNP groups