View source: R/QTL_effect_QxEC.R
QTL_effect_QxEC | R Documentation |
Determination of which parental QTL effect show a significant interaction with the environment. Then, the function try to characterize the nature of the QTLxE effect by estimating the sensitivity of the parental allelic effects showing significant QTLxE interaction to environmental covariates provided by the user.
QTL_effect_QxEC( mppData, trait, env_id = NULL, VCOV = "UN", ref_par = NULL, QTL = NULL, QmainQi = TRUE, thre_QTL = 2, all_main = TRUE, EC, Qmain_QxE = NULL, QTLxEC_plot = TRUE, maxIter = 100, msMaxIter = 100 )
mppData |
An object of class |
trait |
|
env_id |
|
VCOV |
VCOV |
ref_par |
Optional |
QTL |
Object of class |
QmainQi |
|
thre_QTL |
|
all_main |
|
EC |
|
Qmain_QxE |
results from |
QTLxEC_plot |
|
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. |
The function first estimate the parental QTL allele main and QTLxE effect
using the function QTL_effect_main_QxE
. Then it determines
which parental allele shows a significant QTLxE effect by looking if the
-log10(p-val) of the parental QTLxE effect is superior or equal to
thre_QTL
and if the -log10(p-val) of QTLxE term is superior to one of
the main effect. Finally, given this information, the function replaces the
QTLxE term of the parental QTL allelic effect showing a significant QTLxE
effect with a main effect and QTLxEC term representing interaction between
the parental QTL allele and the environmental covariate (EC). The QTLxEC term can
be interpreted as a sensitivity of the QTL to the variation of the EC in the
different environments.
Two options are possible concerning the inclusion of the parental QTL allele
as main effect in the QTLxEC model. Either all parental allele are introduced
(all_main = TRUE
, default), or only the parental allele showing a
singificant main effect are introduced (all_main = FALSE
).
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.
Return:
List
with one data.frame
per QTL that contains the following
elements:
QTL parent allele main effect expressed as deviation with respect to the reference parent
QTL parent allele effect in environment j expressed as deviation with respect to the reference parent
Significance of the parent main effect expressed as the -log10(p-val)
Significance of the parent QTLxE effect expressed as the -log10(p-val)
Vincent Garin
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>.
QTL_effect_main_QxE
## Not run: data(mppData_GE) Qpos <- c("PZE.105068880", "PZE.106098900") EC <- matrix(c(180, 310, 240, 280), 4, 1) rownames(EC) <- c('CIAM', 'TUM', 'INRA', 'KWS') colnames(EC) <- 'cum_rain' Qeff <- QTL_effect_QxEC(mppData = mppData_GE, trait = c('DMY_CIAM', 'DMY_TUM', 'DMY_INRA_P', 'DMY_KWS'), env_id = c('CIAM', 'TUM', 'INRA', 'KWS'), QTL = Qpos, EC = EC) Qeff ## End(Not run)
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