examplePhi: Simulation experiment

In thoree/kinBoot: Bootstrapping and kinship estimation

Simulation experiment

Description

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

Usage

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

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
case	Logical. Describes experiment. #'

Details

See bootPhi()

Value

Returns a data frame summarising the simulation.

Examples

library(forrel)
library(ribd)
library(coxed) # for bca confidence intervals

peds = list(quadHalfFirstCousins(), doubleFirstCousins(), nuclearPed(2),
            halfSibPed(), cousinPed(1))
names(peds) = c("QHFC",  "DFC", "S", "H", "FC")
idlist = lapply(peds, leaves)
# phi = unlist(lapply(peds, function(x) kinship(x, leaves(x))))
N = 1; B = 4 # Increase to N = 100 and B = 1000, at least
seed = 1729
# Example 1a Many SNP-s. Intended to meet assumptions well
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, case = "1000snps")

# Example 1b NorwegianFrequency. Medium number of markers
db = NorwegianFrequencies
res2 = examplePhi(peds, idlist, N = N, B = B, seed = seed, db = db, case ="Norwegian")

# Example 1c Few markers, 8 CODIS markers
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, case = "codis8")
# Example 1d
db1 = NorwegianFrequencies[c("SE33")]
res4 = examplePhi(peds, idlist, N = N, B = B, seed = seed,
                  db = db1, case = "db1")

# Example 1e
n = 10 # no of markers
p = 0.5
freq = list()
for (i in 1:(n-1))
     freq[[i]] =  list(afreq = c("1" = p, "2" = 1- p))
p = rep(1/100,100)
names(p) = 1:100
freq[[10]] = list(afreq = p)
res5 = examplePhi(peds, idlist, N = N, B = B, seed = seed,
                db = freq, case = "nonid")

 res = rbind(res1, res2, res3, res4, res5)
 save(res, file = "res27mar.Rdata")

thoree/kinBoot documentation built on Nov. 22, 2022, 6:31 p.m.