Below I explore the profileSim function and rearrange

Rearranging `profileSim` output about forrel HOT 2 CLOSED

thoree commented on June 28, 2024

Rearranging `profileSim` output

from forrel.

Comments (2)

magnusdv commented on June 28, 2024

Ok, nice example. I see that the output of profileSim() was not optimal. I have modified this now, so that you don't have to reorganise manually.

Below is my version of the code, with a couple of simplifications:

The seed can be set in the function call
By default all indivis are included (so the ids parameter is not necessary in this case)
Since the only difference between ch and fa is the label, you can make ch in one line using relabel().
The transferMarkers() part is a one-liner!

library(forrel, quietly = T)

### F and C unrelated singletons
fa = singleton("F")
fa = setMarkers(fa, marker(fa, name = "L1"))
ch = relabel(fa, "C")

# Simulate 5 profiles
simUN = profileSim(list(fa, ch), N = 5, cond = "L1", seed = 123)

# LRs
LR(simUN, 1)$likelihoodsPerSystem
#>    [,1]  [,2] [,3]   [,4] [,5]
#> L1 0.25 0.125 0.25 0.0625 0.25

### F is the true father
x = nuclearPed(1, father = "F", children = "C")

# Transfer genotypes from each sim
simPO = lapply(simUN, function(s) transferMarkers(s, x))

# LRs
LR(simPO, 1)$likelihoodsPerSystem
#>    [,1]  [,2] [,3] [,4] [,5]
#> L1 0.25 0.125 0.25    0 0.25