EC_effect: Determine EC effects

In vincentgarin/mppR: Multi-Parent Population QTL Analysis

Determine EC effects

Description

Determine the effect of environmental covariates (EC) on the mean of a trait across environments and the time range where this effect is the strongest. The procedure was originally proposed by Li et al. (2018).

Usage

EC_effect(
  trait_env_mean,
  crop_duration,
  EC_list,
  type,
  min_win = 20,
  sel_criteria = "global",
  plot = TRUE,
  plot_dir = NULL,
  p_title = "EC_plot",
  env_nm = NULL
)

Arguments

trait_env_mean	vector of trait mean over environment.
crop_duration	numerical value indicating the crop duration.
EC_list	list EC parameter matrix. one per environment. The order of the environment must be the same as the one of the trait mean.
type	character string vector indicating the type of statistic that correspond to the EC. Either the cumulated sum ('sum') or the average ('mean').
min_win	Numerical value indicating the minimum size of the range between start and end day when the EC values are measured. Default = 20
sel_criteria	Character specifying the selection criteria. Default = 'global'
plot	Logical value indicating if a plot of the EC effects over time should be returned. Default = FALSE,
plot_dir	Directory where the plot should be returned. Default = NULL
p_title	Title of the plot. Default = 'EC_plot'
env_nm	Optional vector of environment name. Default = NULL.

Value

Return:

data.frame that contains the following elements for each EC (line). The first line is the value of the EC in the different environments:

1. Start and end date of the optimal window

2. R2 of correlation between trait and EC

3. Direction of the correlation

4. Average R2 value over all tested windows

5. EC value in the different environments for the optimal time window

Author(s)

Vincent Garin

References

Li, X., Guo, T., Mu, Q., Li, X., & Yu, J. (2018). Genomic and environmental determinants and their interplay underlying phenotypic plasticity. Proceedings of the National Academy of Sciences, 115(26), 6679-6684.

vincentgarin/mppR documentation built on March 13, 2024, 7:30 p.m.