QTL_effect_main_QEI {mppR} | R Documentation |
Main and QTL by environment interaction model
Description
The function estimate a QTL model where each parental QTL allelic effect is decomposed into a main effect and a QTL by environment effect (QEI). It allows the user to determine which parental allelic effects have a significant interaction with the environment.
Usage
QTL_effect_main_QEI(
mppData,
trait,
env_id = NULL,
ref_env = NULL,
ref_par = NULL,
VCOV = "UN",
QTL = NULL,
maxIter = 100,
msMaxIter = 100
)
Arguments
mppData |
An object of class |
trait |
|
env_id |
|
ref_env |
Optional |
ref_par |
Optional |
VCOV |
VCOV |
QTL |
Object of class |
maxIter |
maximum number of iterations for the lme optimization algorithm. Default = 100. |
msMaxIter |
maximum number of iterations for the optimization step inside the lme optimization. Default = 100. |
Details
The function estimate the following model
where the QTL effect is decomposed into that represent the
main parental allelic effect across environments and
which is
the QEI effect. allelic effects must be interpreted as deviation with respect
to the reference parent ('ref_par') in the reference environment ('ref_env').
By default the reference parent is the one with the highest allelic frequency
(e.g. central parent in a NAM population).
The estimation is performed using an exact mixed model with function from R
package nlme
. The significance of the allele effect is assessed using a
Wald test.
Value
Return:
List
with one data.frame
per QTL that contains the following
elements:
To be filled
To be filled
Significance of the parent main effect expressed as the -log10(p-val)
Significance of the parent QTLxE effect expressed as the -log10(p-val)
Author(s)
Vincent Garin
References
Pinheiro J, Bates D, DebRoy S, Sarkar D, R Core Team (2021). nlme: Linear and Nonlinear Mixed Effects Models_. R package version 3.1-152, <URL: https://CRAN.R-project.org/package=nlme>.
Examples
## Not run:
data(mppData_GE)
Qpos <- c("PZE.105068880", "PZE.106098900")
Qeff <- QTL_effect_main_QEI(mppData = mppData_GE,
trait = c('DMY_CIAM', 'DMY_TUM', 'DMY_INRA_P', 'DMY_KWS'),
env_id = c('CIAM', 'TUM', 'INRA', 'KWS'),
QTL = Qpos)
Qeff
## End(Not run)