pred_gwas_FBM: Run a GMMAT GWAS on genotype/phenotype data.

In hemstrow/GeneArchEst: Estimate Genomic Architecture for Quantitative Traits

Run a GMMAT GWAS on genotype/phenotype data.

Description

Run a GMMAT GWAS on genotype/phenotype data.

Usage

pred_gwas_FBM(
  x = NULL,
  phenotypes,
  maf = 0.05,
  pass_G = NULL,
  GMMAT_infile = NULL,
  phased = F,
  par = 1,
  center = T
)

Arguments

x	genotype data, default NULL. Genotype with individuals in columns (either 1 or 2 columns per individual for unphased or phased data). Can either be coercable to a matrix or be a FBM.
phenotypes	numeric. Phenotype data, one numeric value per individual, in the same order as the genotype data.
maf	numeric, default 0.05. Minor allele frequency filter to be applied to both G-matrix and GWAS. Ignored if x is NULL.
pass_G	numeric matrix, default NULL. An n x n genetic relatedness matrix. If NULL, calculated from x via Gmatrix using the Yang et al 2010 method.
GMMAT_infile	character, default NULL. If provided, the file path to an infile for glmm.score. If NULL, will be written from x.
phased	logical, default F. Is the data in x phased (in two columns per individual)? Ignored if x is NULL.
par	numeric, default 1. Number of parallel cores to use for G matrix creation. Ignored if x is NULL.
center	logical, default T. If TRUE, the phenotypes will be centered (set to mean 0) prior to GWAS calculation

hemstrow/GeneArchEst documentation built on June 10, 2025, 5:06 a.m.