mppR (version 1.4.0)

QTL_effect_QxEC: Estimation of QTL effect sensitivity to environmental covariates

Description

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.

Usage

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
)

Value

Return:

List with one data.frame per QTL that contains the following elements:

1. QTL parent allele main effect expressed as deviation with respect to the reference parent

2. QTL parent allele effect in environment j expressed as deviation with respect to the reference parent

3. Significance of the parent main effect expressed as the -log10(p-val)

4. Significance of the parent QTLxE effect expressed as the -log10(p-val)

Arguments

mppData

An object of class mppData.

trait

Character vector specifying which traits (environments) should be used.

env_id

Character vector specifying the environment names. By default, E1, ... En

VCOV

VCOV Character expression defining the type of variance covariance structure used. 'CS' for compound symmetry assuming a unique genetic covariance between environments. 'CSE' for cross-specific within environment error term. 'CS_CSE' for both compound symmetry plus cross-specific within environment error term. 'UN' for unstructured environmental variance covariance structure allowing a specific genotypic covariance for each pair of environments. Default = 'UN'

ref_par

Optional Character expression defining the parental allele that will be used as reference for the parental model. Default = NULL

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.

QmainQi

logical value specifying how the QTL parental allele main effects are estimated. For further explanation see the details section. Default = TRUE

thre_QTL

Numerical value specifying the -log10(p-val) threshold for a parental QTL allele to be considered as significant. By default, thre_QTL = 2, which correspond to a p-value of 0.01.

all_main

Logical value specifying if all the parental alleles should be set as main effect in the QTLxEC model or if only the significant parental allele should be introduced in the model as main effect and QTLxEC effect if the QTLxE term is significant. Default = TRUE.

EC

Numeric matrix with environments as row and environmental covariates (EC) as column. The cell i, j of EC specify the value of the jth EC in environment i.

Qmain_QxE

results from QTL_effect_main_QxE

QTLxEC_plot

Logical value specifying if the data to plot sensitivity curve with the function plot_QTLxEC should be returned. Default = TRUE

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.

Author

Vincent Garin

Details

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.

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>.

See Also

QTL_effect_main_QxE

Examples

if (FALSE) {

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

}