assort.mate: assort.mate

In yoki5348/VT_SEM: Vertical-Transmission Structural Equation Modeling (VT-SEM)

Description

VTSEM pakcage is developed to distribute the structural equation model (SEM) for estimating the vertical transmitted environment factors via polygenic risk score (PRS) of Trio data

Arguments

SIMULATE_DAT_GEN

assort.mate <- function(PHENDATA, MATCOR, POPSIZE, avoid.inbreeding=TRUE)

Author(s)

Yongkang Kim ([e-mail]) Jared Balbona Matthew C Keller

Examples

num.cvs <- 100 #The number of causal variants
am <-  0.25 # assortative mating parameter, mu
herit0 <- 0.5 #Inital heritability
vf0 <- 0.15 #Initial variance of vertical transmitted environment factor
######ve0=1-vf0-herit0, so herit0+vf0 must be less than 1
Unequal_AM=TRUE # TRUE: Generating disequilibrium AM dataset, FALSE: Generating equilibrium AM dataset
prop.h2.latent <- 0.5 #Proportion of heritability

seed <- 1234567
max.cores <- 1 ##Number of used cores for OpenMx
num.gen <- 20 #Number of generating generation
pop.size <- 1000 #The number of independent trio dataset
num.its <- 1000
RUN.MARKERS <- FALSE  #whether to only consider GRMs built from CVs (FALSE) or both CVs and SNPs (TRUE)
avoid.inb <- FALSE
save.covariances <- TRUE
save.history <- TRUE

#AM Simulation wildcards
MIN.MAF <- .1
MAX.MAF <- .50

#CVs and their effect sizes
MAF.VECTOR <- runif(num.cvs,MIN.MAF,MAX.MAF)  #Can change the distribution of MAFs here
GENTP.VAR <- MAF.VECTOR*(1-MAF.VECTOR)*2
#ALPHA.VECTOR <- rnorm(CVS,0,sqrt(1/(CVS*GENTP.VAR))) #Can change the distribution of effect sizes here - random effects
ALPHA.VECTOR <- sample(c(-1,1),num.cvs,replace=TRUE)*sqrt(1/(num.cvs*GENTP.VAR)) #Can change the distribution of effect sizes here - fixed f'n of MAF
CV.INFO <- data.frame(MAF=MAF.VECTOR,alpha=ALPHA.VECTOR) #we'll use this for both the observed and latent

assort.mate(PHENDATA=PHEN,  MATCOR=PHENO.MATE.CUR, POPSIZE=POP.CUR, avoid.inbreeding=AVOID.INB)

yoki5348/VT_SEM documentation built on July 24, 2021, 5:10 p.m.