RMP {forensim} | R Documentation |
RMP
computes the random match probability of DNA evidence given in a matrix (or data frame) or
in a text file. Several situations are handled: the suspect and an unknown offender are unrelated,
or are members of the same subpopulation with a given coancestry coefficient theta, or are close
relatives. For the latter case, the relationship is described by the kinship coefficients.
RMP(suspect=NULL, filename=NULL, freq, k=c(1,0,0), theta=0,refpop=NULL)
suspect |
a matrix or a data frame of dimension L x 2, L being the number of loci involved in the DNA
evidence.
The first column gives the loci names, and the second column gives the suspect's genotype
at each locus. A genotype is coded as a character where each string contains two alleles
separated by '/'.
The DNA evidence can also be given in a text file, see argument filename .
|
filename |
the file name from which the input data should be read. Data mut be a matrix of dimension L x 2, L being the number of loci involved in the DNA evidence.The first column gives the loci names, and the second column gives the suspect's genotype at each locus. A genotype is coded as a character where each string contains two alleles separated by '/'. |
freq |
a tabfreq object giving the allele frequencies
|
k |
vector of kinship coefficients (k0, k1, k2), where ki is the probability that two people (the suspect and an unknown offender) will share i alleles identical by descent, i = 0, 1, 2. |
theta |
a float in [0,1[. theta is equivalent to Wright's Fst.
In case of population subdivision, it allows a correction of the allele frequencies in the
subpopulation of interest |
refpop |
the reference population in freq from which to extract the allele frequencies fro the RMP calculation.
This argument is obligatory only if freq contains allele frequencies from several populations
|
The match probability is derived from Balding and Nichols (1994) and is computed as:
k_2 + k_1 Z_1 + k_0 Z_2
where
k_0, k_1, k_2 are the kinship coefficients,
Z_1 is the match probability when the suspect an the unknown offender share one allele identical-by-descent.
Z_2 is the match probability in the unrelated case, when the suspect an the unknown offender share 0 allele
identical-by-descent.
In the homozygous case, with the allele frequency p_i:
Z_1 = (2theta + (1-theta) p_i)/ (1+theta)
Z_2 = [2theta + (1-theta)p_i][3theta + (1-theta)p_i] / [(1 + theta)(1 + 2theta)]
In the heterozygous case, with allele frequencies p_i and p_j:
Z_1 = (2theta + (1-theta) (p_i+p_j))/ (2(1+theta))
Z_2 = 2[theta + (1-theta)p_i][theta + (1-theta)p_j] / [(1 + theta)(1 + 2theta)]
theta is Wright's Fst coefficient, usually called the coancestry coefficient in forensic studies. Main effects of allele dependencies between loci in the suspect's subpopulation are taken into account though the coancestry coefficient, hence, the match probability at all loci is, to a close approximation, the product of single-locus probabilities.
RMP
returns a list with the following components:
RMP.loc |
single-locus match probabilities |
RMP |
multiloci match probability (product of single-locus match probabilities) |
Hinda Haned haned@biomserv.univ-lyon1.fr
Balding DJ, Nichols RA. DNA profile match probability calculation: How to allow for population stratification, relatedness, database selection and single bands. Forensic Sci I 1994;64:125-140.
LR
for the evaluation of DNA evidence through likelihood ratio
# random match probability # data input data <- matrix(c("CSF1PO","FGA","TH01","TPOX","VWA","D3S1358","D5S818", "D7S820","D8S1179","D13S317","D16S539","D18S51","D21S11","D2S1338","D19S433", "12/11","22/19","6/7","10/8","17/18","18/17","12/12","8/8","13/13","11/11", "12/10","14/15","33.2/32.2","23/22","14/14"),nc=2) colnames(data)<- c('locus','genotype') #15-locus genotype data #allele frequencies are taken from the strusa data set data(strusa) RMP(suspect=data,freq=strusa,refpop="Cauc") # using a preexisting file from the forensim package RMP(filename=system.file("files/exprofile.txt", package = "forensim"), freq=strusa,refpop="Cauc")