logLR {KINSIMU}

CLR for a single case

Description

CLR calculation for a single case, where two individual participated and labeled as A and B

Usage

logLR(
  AB,
  afmatrix = NULL,
  rare = NULL,
  allelename = FALSE,
  stepPI = FALSE,
  adelta3 = NULL,
  adelta9 = NULL,
  mu = 0.002
)

Arguments

AB

Genotypes of two individuals in a case, which should be data.frame with 4 columns (2 for each individual) and nl rows, where nl stand for number of loci. The row names should be the name of each locus;

afmatrix

name of allele frequency list, which can be loaded with "EvaluatePanel" function

rare

a data frame containing the frequency of rare allele on the locus, with 1 row and multiple columns, each column for a marker;

allelename

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

stepPI

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 PI if IBS=0 between an alleged PC pair.

adelta3

distributions of the IBD coefficient of the outbred plaintiff's hypotheses in LR calculation, which should be a data.frame with 3 columns and x rows, where x stood for the number of such LR being calculated. The names of columns should be "k0", "k1" and "k2", and those of rows the name of LRs

adelta9

distributions of the Jacquard coefficient of the inbred plaintiff's hypotheses in LR calculation, which should be a data.frame with 9 columns and x rows, where x stood for the number of such LR being calculated. The names of columns should be "D1-D9", and those of rows the name of LRs

mu

mutation rate when paternity index is needed to be calculated, defualts to 0.002.

Value

a list of two data.frames: (i) results_on_each_marker: multiple types of parameters calculated on each marker, including IBS and multiple log10 of LRs; (ii) total_results_of_the _case: the CIBS and log10CLR results for the whole case.

Examples

# example code
AB<-data.frame(a=rep(0,42),b=rep(0,42),c=rep(0,42),d=rep(0,42))
for (i in 1:42) {
temp<-pairsimu(af = FortytwoSTR$afmatrix[[i]],ss = 1,delta = c(0,1,0),allelename = FALSE)
AB[i,]=temp
rownames(AB)[i]=names(FortytwoSTR$afmatrix)[i]
}
adelta3<-data.frame(k0=c(0,0.25,0.5),k1=c(1,0.5,0.5),k2=c(0,0.25,0),row.names = c("PC","FS","HS"))
adelta9<-data.frame(D1=0,D2=0,D3=0,D4=0,D5=0.25,D6=0,D7=0.25,D8=0.5,D9=0,row.names = "FIMCpair")
results<-logLR(AB=AB,afmatrix=FortytwoSTR$afmatrix,rare=FortytwoSTR$rare,stepPI=TRUE,
adelta3=adelta3,adelta9=adelta9)
results$total_results_of_the_case