KINSIMU (version 0.1.2-2)

LRparas: Calculating parameters in LR

Description

Counting and calculating parameters used in the calculation process of different pairwise LR calculation

Usage

LRparas(
  AB,
  af = NULL,
  rare = NULL,
  allelename = FALSE,
  stepwisePI = FALSE,
  bred = FALSE,
  mu = 0.002
)

Value

a data frame with multiple column and ss rows, containing different types of parameters used in different LR calculation according to argument settings

Arguments

AB

Genotypes of two individuals of each case, which should be data.frame with 4 columns (2 for each individual) and ss rows, where ss stand for sample size;

af

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

rare

frequency of rare allele on the locus

allelename

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

stepwisePI

If TRUE, empirical decreasing model of STR mutation would be taken when paternity index is needed to be calculated, otherwise, mutation rate would be taken as PImu if IBS=0 between an alleged PC pair.

bred

if TRUE, parameters used in the calculation of LR in inbred relationship would be calculated

mu

mutation rate for PI calculation, with a default of 0.002

Details

Note that LR elements are in their original values instead of log10 values used in other functions.

Examples

af = FortytwoSTR$afmatrix[[1]]
AB = pairsimu(af = af,ss = 10000,delta = c(0,1,0),allelename = FALSE)
LRelements<-LRparas(AB=AB, af=af, rare=FortytwoSTR$rare[1][1,1],allelename=FALSE,
  stepwisePI=TRUE,bred=TRUE)