pairscan_kin: Run the pairscan with a kinship correction

In TheJacksonLaboratory/CAPE: Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

Run the pairscan with a kinship correction

Description

This function is called by pairscan when a kinship correction is requested. It adjusts each variable according to the kinship matrix using kin_adjust and then fits linear pairwise models to the adjusted data.

Usage

pairscan_kin(
  data_obj,
  geno_obj,
  scan_what,
  marker_pairs,
  kin_obj,
  verbose = FALSE,
  run_parallel = FALSE,
  n_cores = 2
)

Arguments

data_obj	a Cape object
geno_obj	a genotype object
scan_what	A character string uniquely identifying whether eigentraits or raw traits should be scanned. Options are "eigentraits", "raw_traits"
marker_pairs	A two-column matrix containing the marker pairs to be tested.
kin_obj	a kinship object
verbose	A logical value indicating whether to print progress to the screen
run_parallel	A logical value indicating whether parallel processing should be used
n_cores	The number of cores to be used if run_parallel is TRUE

Value

This function returns a list with three elements. The elements contain the marker pair effect sizes, the marker pair standard errors, and the covariance matrix for each test. The output is then further processed by pairscan.

TheJacksonLaboratory/CAPE documentation built on Feb. 12, 2024, 4:32 p.m.