rep_peaks: Find peaks and LD blocks in the LMM results

In TheJacksonLaboratory/mousegwas: Run in-bred mouse GWAS

Description

rep_peaks use the individual starins genomtypes matrix to find LD blocks in a greedy way it starts by sorting the GWAS p-values and then choosing the lowest p-value and removing all markers with a high correlation. It then selects the next marker and so on until all markers with p-values smaller than the threshold are in peak regions.

Usage

rep_peaks(
  genotypes,
  gwas_pvs,
  rs_thr = 0.4,
  pthr = 1e-20,
  mxd = 1e+07,
  test = "p_wald"
)

Arguments

genotypes	The genotypes matrix, one column for each strain, used for computing correlations
gwas_pvs	GWAS output pvalues
rs_thr	Threshold for correlation, r^2 larger than this value will be considered same peak
pthr	P-value threshold
mxd	Maximal peak width
test	Test name in the results data frmae

Value

a table with the marker name, choose = peak region number, ispeak = marker is peak, rsq = r square value

TheJacksonLaboratory/mousegwas documentation built on Sept. 27, 2021, 9:14 a.m.