mppGE_back_elim: Backward elimination MPP GxE analysis

In vincentgarin/mppGxE: MPP GxE QTL analysis

Backward elimination MPP GxE analysis

Description

Perform a backward elimination on a list of QTL using a MPP GxE model.

Usage

mppGE_back_elim(
  mppData,
  trait,
  Q.eff = "cr",
  VCOV = "CS_CSRT",
  QTL = NULL,
  alpha = 0.01,
  workspace = 8e+06
)

Arguments

mppData	An object of class mppData.
trait	Character vector specifying which traits (environments) should be used.
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. "ID" for identity, "CSRT" for within environment cross-specific residual terms, "CS_CSRT" for compound symmetry with within environment cross-specific residual terms. Default = "CS_CSRT".
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)

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

QTL <- mppGE_back_elim(mppData = mppData_GE, trait = c('DMY_CIAM', 'DMY_TUM'),
                       Q.eff = 'par', QTL = Qpos)

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