forensim (version 1.1-4)

tabSPH: Builds a matrix of the dropout variable and the corresponding surviving peak heights

Description

The tabSPH function builds a matrix of the dropout variable and the corresponding surviving peak heights, for each available locus or across all loci (default). The constructed matrices have two columns: the dropout variable and the surviving peak heights. The logistic model proposed to model the dropout probability from experimental data (see the references section) can be performed directly on the data yielded by tabSPH.

Usage

tabSPH(x, y = NULL, geno, tabcsv, byloc = FALSE,s=40)

Arguments

x

numeric label of the contributing individual, if the stain is a mixture, x should give the label of the first individual contributing to the mixture

y

numeric label of the second contributing individual, default is NULL. If the stain is a mixture, y should give the label of the second individual contribution to the mixture. This argument is skipped if the stain is not a mixture (default

geno

a matrix giving the genotypes of the individuals contributing to the analyzed data for each locus. An individual genotype is given in rows for each locus in column. A homozygous carrying allele 9 is coded '9/9', a heterozygous carrying alleles 8 and 9

tabcsv

a matrix giving the validation table of the analysed DNA stain. tabcsv must have a ``genemapper'' validation table structure, namely, information about the present alleles and the corresponding peak heights must be given.

byloc

logical indicating whether data should be displayed per locus (TRUE) or overall loci (FALSE, default)

s

numeric giving the detection threshold for alleles in Relative fluorescence units (RFU) , default is set to 40 RFUS. An observed allele with a peak height smaller (

Value

• If argument byloc is TRUE, tabSPH yields a list of length the number of available loci, each elements of the list contain a matrix with two columns:
• D
  the dropout variable
• H
  the surviving peak height
• If argument byloc is FALSE, tabSPH yields a single matrix with columns D and H described above.

Details

Both mixed and unmixed samples can be used in tabSPH, setting the y argument to NULL (default) will produce results considering data for x only. In case of mixtures, note that only heterozygote genotypes with no shared alleles are considered.

References

Gill P, Puch-Solis R, Curran J. The low-template-DNA (stochastic) threshold-Its determination relative to risk analysis for national DNA databases. Forensic Science International: Genetics, 2009, 3, 104-111

See Also

tabDNAproxy

Examples

#load the example data
data(dropdata)
tabcsv<-dropdata$tabcsv
genot<-dropdata$genot
#individuals' labels are 1 and 2
#recording dropout variable matched with the surviving peak heights
#for heterozygotes whith non shared alleles
tabSPH(1,2,geno=genot,tabcsv=tabcsv,s=0)