P_likelihood: Compute likelihoods for populations of origin
In eriqande/SNPcontam: Detecting contaminated samples from SNP genotypes

Compute likelihoods for populations of origin

1	P_likelihood(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 x N numeric matrix which contains the the probabilities the individuals originate from certain populations. The probability that the ith originated from population p is ouput(p,i).

eriqande/SNPcontam documentation built on May 16, 2019, 8:44 a.m.