adjustGRM {RAINBOWR}

Function to adjust genomic relationship matrix (GRM) with subpopulations

Description

Function to adjust genomic relationship matrix (GRM) with subpopulations

Usage

adjustGRM(
  y,
  X = NULL,
  ZETA,
  subpopInfo = NULL,
  nSubpop = 5,
  nPcsFindCluster = 10,
  include.epistasis = FALSE,
  package.MM = "gaston"
)

Arguments

y

A n \times 1 vector. A vector of phenotypic values should be used. NA is allowed.

X

A n \times p matrix. You should assign mean vector (rep(1, n)) and covariates. NA is not allowed.

ZETA

A list of variance matrices and its design matrices of random effects. You can use only one kernel matrix for this function. For example, ZETA = list(A = list(Z = Z.A, K = K.A)) (A for additive) Please set names of lists "Z" and "K"!

subpopInfo

The information on group memberships (e.g., subgroups for the population) will be required. You can set a vector of group names (or clustering ids) for each genotype as this argument. This vector should be factor.

nSubpop

When 'subpopInfo = NULL', 'subpopInfo' will be automatically determined by using find.clusters function. You should specify the number of groups by this argument to decide 'subpopInfo'.

nPcsFindCluster

Number of principal components to be used for 'adegenet::find.clusters'. This argument is used inly when 'subpopInfo' is 'NULL'.

include.epistasis

Whether or not including the genome-wide epistastic effects into the model to adjust ZETA.

package.MM

The package name to be used when solving mixed-effects model. We only offer the following three packages: "RAINBOWR", "MM4LMM" and "gaston". Default package is 'gaston'. See more details at EM3.general.

Value

A List of

$ZETAAdjust

Adjusted ZETA including only one kernel.

$subpopInfo

A vector of 'subpopInfo' used in this function.

$covariates

A matrix of covariates used in the mixed effects model.

#'

$nullModel

Results of mixed-effects model for multiple kernels.

$nSubpop

'nSubpop' used in this function.

$include.epistasis

'include.epistasis' used in this function.

References

Rio S, Mary-Huard T, Moreau L, Bauland C, Palaffre C, et al. (2020) Disentangling group specific QTL allele effects from genetic background epistasis using admixed individuals in GWAS: An application to maize flowering. PLOS Genetics 16(3): e1008241.