Description Usage Arguments Value
Compute likelihoods for populations of origin
1 | Pcontam(snp_zeroes, snp_ones, genos, lambda)
|
snp_zeroes |
Matrix of counts of the "zero" allele at L SNPs in P populations. This is an L x P integer matrix where L is the number of SNP loci and P is the number of populations in the baseline. The observed number of 0 alleles at locus j in population p is snp_zeroes[j,p] |
snp_ones |
Same as above, but for the 1 allele at each SNP. |
genos |
Matrix of the genotypes of N individuals at each of the L loci. Genotypes are represented as the number of "1" alleles. This is an L x N integer matrix. The genotype of the ith individual at the locus j is genos(j,i). |
lambda |
The parameter of the beta distribution for the frequency of the "1" allele. |
Returns a P*P x N numeric matrix which contains the the probabilities that contaminated individuals originated from certain combintations of two populations. The probability that the ith individual's contamination originated from population p1 and p2 is ouput(N*(p1-1) + p2,i) + output(N*(p2-1) + p1,i) if p1 and p2 are different populations and output(N*(p1-1) + p1,i) if p1 and p2 are the same population.
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