nei_lm: Standard linear models for testing self and neighbor effects

Description

A function to provide coefficients and p-values of self and neighbor effects for each marker.

nei_lm(
  geno,
  g_nei,
  pheno,
  addcovar = NULL,
  response = c("quantitative", "binary"),
  n_core = 1L,
  asym = FALSE
)

A data.frame including coefficients and p-values of self and neighbor effects, without the chromosome numbers and marker position.

beta_self coefficient for self effects
beta_self coefficient for neighbor effects
p_self p-value for self effects by a likelihood ratio test between a null and standard linear model
p_nei p-value for neighbor effects by a likelihood ratio test between models with or without neighbor effects

geno: An individual x marker matrix. Bialleles (i.e., A or a) must be converted into -1 or 1 digit.
g_nei: An output of nei_coval() object, namely an individual x marker matrix including neighbor genotypic identity.
pheno: A numeric vector including phenotypes for individuals
addcovar: An optional matrix including additional non-genetic covariates. It contains no. of individuals x no. of covariates.
response: An option to select if the phenotype is a "quantitative" trait subject to linear models, or a "binary" trait subject to logistic models.
n_core: No. of cores for a multi-core computation. This does not work for Windows OS. Default is a single-core computation.
asym: If TRUE, asymmetric neighbor effects are also tested and returned as "beta_sxn" and "p_sxn".

This function is a subset of neiGWAS(). nei_lm() gives detailed results when the option model="lm" is selected in neiGWAS().