mppGE_oneS_back_elim: Backward elimination of one stage MPP GxE analysis

In vincentgarin/mppGxE: MPP GxE QTL analysis

Backward elimination of one stage MPP GxE analysis

Description

Backward elimination on a list of QTL using a one stage MPP GxE model.

Usage

mppGE_oneS_back_elim(
  plot_data,
  mppData,
  trait,
  Q.eff = "cr",
  VCOV = "CS_CSRT",
  exp_des_form,
  QTL = NULL,
  alpha = 0.01,
  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.
alpha	Numeric value indicating the level of significance for the backward elimination. Default = 0.01.
workspace	Size of workspace for the REML routines measured in double precision words (groups of 8 bytes). The default is workspace = 8e6.

Value

Return:

QTL	Data.frame of class QTLlist with five columns : 1) QTL marker names; 2) chromosomes; 3) interger position indicators on the chromosome; 4) positions in centi-Morgan; and 5) -log10(p-values).

Author(s)

Vincent Garin

Examples

library(asreml)

data(mppData_GE)
data(plot_data)

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

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

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