mppGE_oneS_QTL_effects: MPP GxE one stage QTL genetic effects

In vincentgarin/mppGxE: MPP GxE QTL analysis

MPP GxE one stage QTL genetic effects

Description

Compute MPP GxE one stage QTL genetic effects.

Usage

mppGE_oneS_QTL_effects(
  plot_data,
  mppData,
  trait,
  Q.eff = "cr",
  VCOV = "CS_CSRT",
  exp_des_form,
  QTL = NULL,
  workspace = 8e+06
)

Arguments

plot_data	Data.frame containing the plot data with the following columns: the trait(s), 'genotype' (genotype indicator), 'check' (check indicator), 'cross' (cross indicator), 'env' (environment indicator), and all other experimental design covariates (e.g. replicate, blocks, etc.). The column names must be ('genotype', 'check', 'cross', env'). The names of the experimental design covariates must be the same as the one used in 'exp_des_form'. For more details see plot_data.
mppData	Object of class mppData contaning the the same genotype identifiers as the one in plot_data ('genotype').
trait	Character expression for the trait matching the trait column in 'plot_data' argument.
Q.eff	Character expression indicating the assumption concerning the QTL effects: 1) "cr" for cross-specific; 2) "par" for parental; 3) "anc" for ancestral; 4) "biall" for a bi-allelic. Default = "cr".
VCOV	VCOV Character expression defining the type of variance covariance structure used: a) "CSRT" for within environment cross-specific residual terms; b) "CS_CSRT" for compound symmetry with within environment cross-specific residual terms. Default = "CS_CSRT".
exp_des_form	Character expression for the random experimental design effects in asreml-R format. For example, 'env:replicate + env:replicate:block'. The variable names used in 'exp_des_form' should strictly match the column names used in 'plot_data'.
QTL	Object of class QTLlist representing a list of selected marker positions obtained with the function QTL_select() or a vector of character marker positions names. Default = NULL.
workspace	Size of workspace for the REML routines measured in double precision words (groups of 8 bytes). The default is workspace = 8e6.

Value

Return:

Qeff	List of data.frame (one per QTL) containing the following information: QTL genetic effects Standard error of the QTL effects. Test statistics of the effects (Wald statistic). P-value of the test statistics. Significance of the QTL effects.

Author(s)

Vincent Garin

Examples

library(asreml)

data(mppData_GE)
data(plot_data)

Qpos <- c("PZE.105068880", "PZE.106098900")

Qeff <- mppGE_oneS_QTL_effects(plot_data = plot_data, mppData = mppData_GE,
                              trait = 'DMY', Q.eff = 'par',
                              exp_des_form = 'env:Rep + env:Rep:Block',
                              QTL = Qpos)

Qeff

vincentgarin/mppGxE documentation built on June 25, 2022, 2:45 p.m.