Group SNPs; adapted from group.multi by Chris Wallace

Group SNPs; adapted from group.multi by Chris Wallace

groupmultiU(
  SM2,
  snp.data,
  is.snpmat,
  min.mppi = 0.01,
  minsnpmppi = 0.01,
  r2.minmerge = 0.6
)

Arguments

SM2

snpmod object

snp.data

SnpMatrix or SNP covariance matrix with snp ids as column names

is.snpmat

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

min.mppi

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

minsnpmppi

only group snps with total MPPI > minsnpmppi

r2.minmerge

merge groups with minimum between-group r2 > r2.minmerge

Value

list with three components.

First is a data.frame with each row giving summary statistics for each group.

Second is a groups object, each elements ordered according to the rows of the summary

Third is the r2 matrix calculated.