PE: Exclusion probabilities

In fam2r: From 'Familias' to R

Description

This is a wrapper for exclusionPower. The probability of exclusion (PE) is calculated for each marker and combined for all markers.

Usage

PE(pedigrees, datamatrix, loci, claim = 1, true = 2, available = NULL, 
  file = NULL, ignore = FALSE)

Arguments

pedigrees	A FamiliasPedigree object or a list of such.
datamatrix	A data frame, each row gives the genotype of one individual, a pair of columns represents a marker.
loci	A FamiliasLocus object or a list of such.
claim	Integer. Index of the claimed pedigree, typically the one where MP=POI.
true	Integer. Index of the assumed true pedigree for PE calculation, typically the one where POI is assumed to be an unrelated individual.
available	Character or integer identifying person to be simulated.
file	Charachter. If not NULL, a file is written.
ignore	Logical. If TRUE, mutations are ignored.

Details

Wrapper for exclusionPower

Value

A data frame. The first column gives the name of the markers, the second the PE. The last line gives the combined result for all markers.

Author(s)

Thore Egeland <[e-mail]>

References

Egeland, Pinto and Vigeland (2014).

See Also

exclusionPower

Examples

data(F21)
pedigrees = F21$pedigrees
datamatrix = F21$datamatrix
loci = F21$loci
available = "Missing Person"
PE(pedigrees, datamatrix, loci, claim = 1, true = 2, 
  available = available, file = NULL)

Example output

Loading required package: Familias
Loading required package: kinship2
Loading required package: Matrix
Loading required package: quadprog
Loading required package: paramlink
Loading required package: Rsolnp
     marker         PE
1   D3S1358 0.52136317
2      TH01 0.00000000
3    D21S11 0.16988273
4    D18S51 0.47672909
5   PENTA E 0.00000000
6    D5S818 0.00000000
7   D13S317 0.00000000
8    D7S820 0.00000000
9   D16S539 0.00000000
10   CSF1PO 0.08965897
11  PENTA D 0.18889470
12      VWA 0.00000000
13  D8S1179 0.19612518
14     TPOX 0.19250700
15      FGA 0.41761726
16  D19S433 0.20519893
17  D1S1656 0.00000000
18  D12S391 0.28118534
19  D2S1338 0.50620741
20  D6S1043 0.00000000
21 D22S1045 0.03481956
22   D2S441 0.21436900
23     SE33 0.00000000
24 D10S1248 0.23619600
25 Combined 0.99051760

fam2r documentation built on May 2, 2019, 1:09 p.m.