examplePhi: Example: bootstrap confidence intervals

In thoree/inbred: Different functions related to LR, bootstrap etc

Description

We consider parametric and nonparametric bootstrap and the kinship coefficient for some pedigrees.

Usage

examplePhi(
  peds,
  idlist,
  N = 2,
  B = 10,
  CItype = "bca",
  conf.level = 0.95,
  seed = NULL,
  verbose = TRUE,
  db = NULL
)

Arguments

peds	list of ped objects with allele frequencies.
idlist	list of ids of of pair.
N	Integer. No of simulations.
B	Integer. No of bootstraps.
CItype	Logical
conf.level	Double
seed	Integer
verbose	Logical
db	database

Details

See note coverage.pdf

Value

Returns

Examples

peds = list(quadHalfFirstCousins(), doubleFirstCousins(), nuclearPed(2),
            halfSibPed(), cousinPed(1))
names(peds) = c("QHFC",  "DFC", "S", "H", "FC")
phi = unlist(lapply(peds, function(x) kinship(x, leaves(x))))
idlist = lapply(peds, leaves)
N = 1; B = 1000; seed = 1729
# Example 1 Many snps
n = 1000 # no of markers
p = rep(0.5, n)
freq = list()
for (i in 1:n)
freq[[i]] =  list(afreq = c("1" = p[i], "2" = 1- p[i]))
db = freq
res1 = examplePhi(peds, idlist, N = N, B = B, seed = seed, db = db)

# Example 2 Norwegian
db = NorwegianFrequencies
res2 = examplePhi(peds, idlist, N = N, B = B, seed = seed, db = db)

# Example Few Codis8
codis8 = c("CSF1PO", "D3S1358", "D5S818", "D7S820", "D8S1179", "D13S317", "D16S539", "D18S51")
db = NorwegianFrequencies[codis8]
res3 = examplePhi(peds, idlist, N = N, B = B, seed = seed, db = db)
res = rbind(res1, res2, res3)
res

thoree/inbred documentation built on March 28, 2021, 7:42 p.m.