Group SNPs; adapted from group.multi by Chris Wallace

Source: R/group.multi.R

Group SNPs; adapted from group.multi by Chris Wallace

groupmulti(
  SM2,
  snp.data,
  is.snpmat,
  min.mppi = 0.01,
  minsnpmppi = 0.01,
  r2.minmerge = 0.5
)

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.