groupmulti: Group SNPs; adapted from group.multi by Chris Wallace

In jennasimit/flashfm: flexible and shared information fine-mapping

Group SNPs; adapted from group.multi by Chris Wallace

Description

Group SNPs; adapted from group.multi by Chris Wallace

Usage

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.

jennasimit/flashfm documentation built on July 31, 2022, 7:32 p.m.