KINSIMU (version 0.1.2-2)

IICAL: Incest index

Description

Calculation of the ratio for a parent-child pair between the probability that the child's other parent is a relative of the present parent to the probability that the child's parents are unrelated

Usage

IICAL(Parent, Child, af, rare = NULL, allelename = FALSE, phi = 0.25)

Value

a data.frame containing 2 columns: Ngs (the genotype similarity score, 1 if both of the two alleles in child's genotype can be inherited from the mother) and Log10LR for each simulation

Arguments

Parent

Genotypes of individual A of each case, which should be data.frame with 2 columns and ss rows, where ss stand for sample size

Child

Genotypes of individual B of each case, which should be data.frame with 2 columns and ss rows, where ss stand for sample size

af

name of allele frequency matrix, a data.frame of 1 column with the allele name being row names

rare

frequency of rare allele

allelename

if TRUE, the input genotype data would be regarded as allelenames, otherwise, the position in the af matrix

phi

kinship coefficent between the parents under Hp (that under Hd euquals to 0),with a defualt of 0.25, i.e., father-daughter incest or full-sibling incest

Details

The premise of using this function should be the confirmation of the parent-child relationship between the two individuals, if there is no sharing alleles between them, 1-2phi would be regarded as the output

Examples

# Simulate 10,000 mother-child pairs with father-daughter incest with pedisimu() function
# based on the 42 STRs in "FortytwoSTR" data.
pedi<-data.frame(Person=c("F","M","C"),Father=c("RI","F","F"),Mother=c("RI","RI","M"))
II_1=II_2=data.frame(Ngs=rep(0,10000),IIphi=rep(0,10000))
for (i in 1:42) {
Genotype1<-pedisimu(af = FortytwoSTR$afmatrix[[i]],ss = 10000,pedi = pedi)
# Calculate II for each case.
II_1<-II_1+IICAL(Parent = Genotype1[,3:4],Child = Genotype1[,5:6],af=FortytwoSTR$afmatrix[[i]],
rare=FortytwoSTR$rare[i][1,1],phi=0.25)
#Simulate 10,000 non-inbred mother-child pairs
Genotype2<-pairsimu(af = FortytwoSTR$afmatrix[[i]],ss = 10000,delta = c(0,1,0),allelename = FALSE)
II_2<-II_2+IICAL(Parent = Genotype2[,1:2],Child = Genotype2[,3:4],af=FortytwoSTR$afmatrix[[i]],
rare=FortytwoSTR$rare[i][1,1],phi=0.25)
}
# histograms of CII distributions in the two groups
xmin<-floor(min(min(II_1$IIphi),min(II_2$IIphi)))
xmax<-ceiling(max(max(II_1$IIphi),max(II_2$IIphi)))
par(mfrow = c(1,2))
hist(II_2$IIphi,xlab = expression(log[10]~CII),main = "Non-inbreed cases",
xlim = c(xmin,xmax), col = "red")
hist(II_1$IIphi,xlab = expression(log[10]~CII),main = "Inbreed cases",
xlim = c(xmin,xmax), col = "blue")