gxe-mr

Background

---

library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

library(simulateGP)

make_gxe <- function(g, e, b_add, b_int, b_e) {
    n <- length(g)
    stopifnot(length(g) != length(e))
    y <- g * b_add + e * b_e + g * e * b_int
    r <- rnorm(n, 0, sqrt(1 - var(y)))
    y <- y + r
    return(y)
}

sim <- function(nid, nsnp, b_add, b_e, b_int, pop_diff) {
    g1 <- rbinom(nid, 2, 0.5)
    g2 <- rbinom(nid, 2, sample(c(-1, 1), 1) * pop_diff + 0.5)

    mean_e <- 

    e1 <- rnorm(nid, 0, 1)
    e2 <- rnorm(nid, sample(c(-1, 1), 1) * pop_diff, 1)


}


params <- expand.grid(
    nid = 10000,
    nsnp = 100,
    b_add = 0.05,
    b_e = 0.05,
    b_int = c(0, 0.025, 0.05),
    pop_diff = seq(0, 0.5, by=0.1)
)
params

     nid nsnp b_add  b_e b_int pop_diff
1  10000  100  0.05 0.05 0.000      0.0
2  10000  100  0.05 0.05 0.025      0.0
3  10000  100  0.05 0.05 0.050      0.0
4  10000  100  0.05 0.05 0.000      0.1
5  10000  100  0.05 0.05 0.025      0.1
6  10000  100  0.05 0.05 0.050      0.1
7  10000  100  0.05 0.05 0.000      0.2
8  10000  100  0.05 0.05 0.025      0.2
9  10000  100  0.05 0.05 0.050      0.2
10 10000  100  0.05 0.05 0.000      0.3
11 10000  100  0.05 0.05 0.025      0.3
12 10000  100  0.05 0.05 0.050      0.3
13 10000  100  0.05 0.05 0.000      0.4
14 10000  100  0.05 0.05 0.025      0.4
15 10000  100  0.05 0.05 0.050      0.4
16 10000  100  0.05 0.05 0.000      0.5
17 10000  100  0.05 0.05 0.025      0.5
18 10000  100  0.05 0.05 0.050      0.5

sessionInfo()

R version 4.5.2 (2025-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.2

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/London
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] simulateGP_0.1.3 dplyr_1.1.4     

loaded via a namespace (and not attached):
 [1] digest_0.6.39     R6_2.6.1          fastmap_1.2.0     tidyselect_1.2.1 
 [5] xfun_0.54         magrittr_2.0.4    glue_1.8.0        tibble_3.3.0     
 [9] knitr_1.50        pkgconfig_2.0.3   htmltools_0.5.8.1 rmarkdown_2.30   
[13] generics_0.1.4    lifecycle_1.0.4   cli_3.6.5         vctrs_0.6.5      
[17] compiler_4.5.2    tools_4.5.2       pillar_1.11.1     evaluate_1.0.5   
[21] yaml_2.3.11       rlang_1.1.6       jsonlite_2.0.0    htmlwidgets_1.6.4