exclusionPower: Power of exclusion

In paramlink: Parametric Linkage and Other Pedigree Analysis in R

Power of exclusion

Description

Computes the power (of a single marker) of excluding a claimed relationship, given the true relationship.

Usage

exclusionPower(
  ped_claim,
  ped_true,
  ids,
  markerindex = NULL,
  alleles = NULL,
  afreq = NULL,
  known_genotypes = list(),
  Xchrom = FALSE,
  plot = TRUE
)

Arguments

ped_claim	a linkdat object, or a list of several linkdat and/or singleton objects, describing the claimed relationship. If a list, the sets of ID labels must be disjoint, that is, all ID labels must be unique.
ped_true	a linkdat object, or a list of several linkdat and/or singleton objects, describing the true relationship. ID labels must be consistent with ped_claim.
ids	individuals available for genotyping.
markerindex	NULL, or a single numeric indicating the index of a marker of ped_claim from which alleles, afreq and known_genotypes will be extracted.
alleles	a numeric or character vector containing marker alleles names. Ignored if markerindex is non-NULL.
afreq	a numerical vector with allele frequencies. An error is given if they don't sum to 1 (rounded to 3 decimals). Ignored if markerindex is non-NULL.
known_genotypes	list of triplets (a, b, c), indicating that individual a has genotype b/c. Must be NULL if markerindex is non-NULL.
Xchrom	a logical: Is the marker on the X chromosome? Ignored if markerindex is non-NULL.
plot	either a logical or the character 'plot_only', controlling if a plot should be produced. If 'plot_only', a plot is drawn, but no further computations are done.

Details

This function computes the 'Power of exclusion', as defined and discussed in (Egeland et al., 2014).

Value

A single numeric value. If plot='plot_only', the function returns NULL after producing the plot.

References

T. Egeland, N. Pinto and M. D. Vigeland, A general approach to power calculation for relationship testing. Forensic Science International: Genetics 9 (2014): 186-190. DOI:10.1016/j.fsigen.2013.05.001

Examples

############################################
### A standard case paternity case:
### Compute the power of exclusion when the claimed father is in fact unrelated to the child.
############################################

claim = nuclearPed(noffs=1, sex=2)     # Specifies individual 1 as the father of 3
true = list(singleton(id=1,sex=1), singleton(id=3, sex=2))     # Specifies 1 and 3 as unrelated
available = c(1, 3)     # Individuals 1 and 3 are available for genotyping

# Equifrequent autosomal SNP:
PE1 = exclusionPower(claim, true, available, alleles = 2, afreq=c(0.5,0.5))

# If the child is known to have genotype 1/1:
PE2 = exclusionPower(claim, true, available, alleles = 2, afreq=c(0.5,0.5),
                     known_genotypes=list(c(3,1,1)))

# Equifrequent SNP on the X chromosome:
PE3 = exclusionPower(claim, true, available, alleles = 2, afreq=c(0.5,0.5), Xchrom=TRUE)

stopifnot(PE1==0.125, PE2==0.25, PE3==0.25)

############################################
### Example from Egeland et al. (2012):
### Two females claim to be mother and daughter. Below we compute the power of various
### markers to reject this claim if they in reality are sisters.
############################################

mother_daughter = nuclearPed(1, sex = 2)
sisters = relabel(nuclearPed(2, sex = c(2, 2)), c(101, 102, 2, 3))

# Equifrequent SNP:
PE1 = exclusionPower(ped_claim = mother_daughter, ped_true = sisters, ids = c(2, 3),
                     alleles = 2)

# SNP with MAF = 0.1:
PE2 = exclusionPower(ped_claim = mother_daughter, ped_true = sisters, ids = c(2, 3),
                     alleles = 2, afreq=c(0.9, 0.1))

# Equifrequent tetra-allelic marker:
PE3 = exclusionPower(ped_claim = mother_daughter, ped_true = sisters, ids = c(2, 3),
                     alleles = 4)

# Tetra-allelic marker with one major allele:
PE4 = exclusionPower(ped_claim = mother_daughter, ped_true = sisters, ids = c(2, 3),
                     alleles = 4, afreq=c(0.7, 0.1, 0.1, 0.1))

stopifnot(round(c(PE1,PE2,PE3,PE4), 5) == c(0.03125, 0.00405, 0.08203, 0.03090))

####### How does the power change if the true pedigree is inbred?
sisters_LOOP = addParents(sisters, 101, father = 201, mother = 202)
sisters_LOOP = addParents(sisters_LOOP, 102, father = 201, mother = 203)

# Equifrequent SNP:
PE5 = exclusionPower(ped_claim = mother_daughter, ped_true = sisters_LOOP,
                     ids = c(2, 3), alleles = 2)

# SNP with MAF = 0.1:
PE6 = exclusionPower(ped_claim = mother_daughter, ped_true = sisters_LOOP,
                     ids = c(2, 3), alleles = 2, afreq=c(0.9, 0.1))

stopifnot(round(c(PE5,PE6), 5) == c(0.03125, 0.00765))

## Not run: 
# Equifrequent tetra-allelic marker:
PE7 = exclusionPower(ped_claim = mother_daughter, ped_true = sisters_LOOP,
                     ids = c(2, 3), alleles = 4)

# Tetra-allelic marker with one major allele:
PE8 = exclusionPower(ped_claim = mother_daughter, ped_true = sisters_LOOP,
                     ids = c(2, 3), alleles = 4, afreq=c(0.7, 0.1, 0.1, 0.1))

stopifnot(round(c(PE7,PE8), 5) == c(0.07617, 0.03457))

## End(Not run)

paramlink documentation built on April 15, 2022, 9:06 a.m.