mmer_adapted: Adapt to sommer MNR core function

In qtlpoly: Random-Effect Multiple QTL Mapping in Autopolyploids

Description

Adapts genomic incidence and relationship (varcov) matrices to run using sommer's C++ core function (v. 4.0 or higher) Function adapted from sommer v. 3.6 (Author: Giovanny Covarrubias-Pazaran)

Usage

mmer_adapted(
  Y,
  X = NULL,
  Z = NULL,
  R = NULL,
  W = NULL,
  method = "NR",
  init = NULL,
  iters = 20,
  tolpar = 0.001,
  tolparinv = 1e-06,
  draw = FALSE,
  silent = FALSE,
  constraint = TRUE,
  EIGEND = FALSE,
  forced = NULL,
  IMP = FALSE,
  complete = TRUE,
  check.model = TRUE,
  restrained = NULL,
  REML = TRUE,
  init.equal = TRUE,
  date.warning = TRUE,
  verbose = FALSE
)

Arguments

void	internal function to be documented

Author(s)

Gabriel de Siqueira Gesteira, [e-mail]

References

Covarrubias-Pazaran G (2016) Genome-assisted prediction of quantitative traits using the R package sommer. PLoS ONE 11 (6): 1–15. doi: 10.1371/journal.pone.0156744.

Pereira GS, Gemenet DC, Mollinari M, Olukolu BA, Wood JC, Mosquera V, Gruneberg WJ, Khan A, Buell CR, Yencho GC, Zeng ZB (2020) Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population, Genetics 215 (3): 579-595. doi: 10.1534/genetics.120.303080.

qtlpoly documentation built on Jan. 12, 2022, 5:06 p.m.