data-raw/create_study_peds.R

In simrvprojects/SimRVSequences: Simulate Genetic Sequence Data for Pedigrees

# load the SimRVPedigree library
library(SimRVPedigree)

#Create hazard object from AgeSpecific_Hazards data
data(AgeSpecific_Hazards)
my_HR = hazard(AgeSpecific_Hazards)

# load libraries needed to simulate pedigrees in parallel.
library(doParallel)
library(doRNG)

npeds <- 5    #set the number of pedigrees to generate

cl <- makeCluster(5)   # create cluster
registerDoParallel(cl) # register cluster


#simulate a sample of five pedigrees using foreach
study_peds = foreach(i = seq(npeds), .combine = rbind,
                     .packages = c("SimRVPedigree"),
                     .options.RNG = 84405180
) %dorng% {
  # Simulate pedigrees ascertained for at least three disese-affected individuals,
  # according to the age-specific hazard rates in the `AgeSpecific_Hazards` data
  # set, ascertained from 1980 to 2010, with seed-founder birth year spanning
  # from 1900 to 1920, stop year set to 2018, and with genetic relative-risk 50.
  sim_RVped(hazard_rates = my_HR,
            GRR = 50, FamID = i,
            RVfounder = TRUE,
            founder_byears = c(1900, 1920),
            ascertain_span = c(1980, 2010),
            stop_year = 2018,
            recall_probs = c(1, 0.5, 0),
            num_affected = 3)[[2]]}

stopCluster(cl) #shut down cluster

difftime(stop_time, start_time, units = "mins")

# win.graph(h = 20, w = 35)
# par(mfrow = c(2, 3))
# plot(study_peds[study_peds$FamID == 1,], ref_year = 2018)
# plot(study_peds[study_peds$FamID == 2,], ref_year = 2018)
# plot(study_peds[study_peds$FamID == 3,], ref_year = 2018)
# plot(study_peds[study_peds$FamID == 4,], ref_year = 2018)
# plot(study_peds[study_peds$FamID == 5,], ref_year = 2018)

#create a sporadic pedigree for example in vignette
study_peds$DA2[study_peds$FamID == 2] = 0

save(study_peds, file="data/study_peds.rdata", compress='xz')
getwd()