Old Stuff On CLM Model

Baby example - 'Evett' data set

alleles<-list(
    D8=c('10','11','14','x'),
    D18=c('13','16','17','x'),
    D21=c('A','B','C','D','x'),
    FGA=c('A','B','C','x'),
    Tho1=c('A','B','C','x'),
    vwa=c('A','B','C','D','x')
    )

freqs<-list(
    D8=c(0.094,0.066,0.209,0.631),
    D18=c(0.125,0.137,0.115,0.623),
    D21=c(0.031,0.258,0.069,0.090,0.552),
    FGA=c(0.187,0.165,0.139,0.509),
    Tho1=c(0.108,0.304,0.000,0.588),
    vwa=c(0.216,0.270,0.219,0.093,0.202)
    )

evidence<-list(
    D8='10-14',
    D18='13-13',
    D21='C-D',
    FGA='A-B',
    Tho1='A-B',
    vwa='A-C'
    )

relweight<-list(
    D8=c(0.4347,0.0285,0.5368,0),
    D18=c(0.8871,0.0536,0.0592,0),
    D21=c(0.0525,0.0676,0.4284,0.4515,0),
    FGA=c(0.5699,0.3908,0.0393,0),
    Tho1=c(0.4015,0.5985,0,0),
    vwa=c(0.4170,0.0884,0.4747,0.0199,0)
)

Amending DNAmixture database format to use these frequencies

Evett<-USCaucasian2
Evett[Evett$marker=="D8S1179"&Evett$allele%in%c(10,11,14),3]<-c(0.094,0.066,0.209)
Evett[Evett$marker=="D18S51"&Evett$allele%in%c(13,16,17),3]<-c(0.125,0.137,0.115)
Evett[Evett$marker=="D21S11"&Evett$allele%in%c(27,30,31,32.2),3]<-c(0.031,0.258,0.069,0.090)
Evett[Evett$marker=="FGA"&Evett$allele%in%c(21,22,23),3]<-c(0.187,0.165,0.139)
Evett[Evett$marker=="TH01"&Evett$allele%in%c(8,9.3),3]<-c(0.108,0.304)
Evett[Evett$marker=="VWA"&Evett$allele%in%c(16,17,18,19),3]<-c(0.216,0.270,0.219,0.093)
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