Description Usage Arguments Details Value

This function computes the similarity scores between the sample SNPs and the haplotype's reference.

1 2 3 4 5 6 7 8 9 | ```
classifSNPs(
genos,
R2,
refs,
alleletable,
BPPARAM = BiocParallel::SerialParam()
)
classifSNPsImpute(genos, R2, refs, BPPARAM = BiocParallel::SerialParam())
``` |

`genos` |
Matrix with the samples genotypes. It is the result of |

`R2` |
Vector with the R2 between the SNPs and the inversion status. |

`refs` |
List of matrices. Each matrix has, for an SNP, the frequencies of each genotype in the different haplotypes. |

`alleletable` |
Data frame with the reference alleles computed with |

`BPPARAM` |
A |

classifSNPs computes, for each individual, similarity scores for all the present haplotypes. For each SNP, we compute as many similarity scores as haplotypes present in the reference. We have defined the similarity score as the frequency of this genotype in the different haplotype population. To compute the global similarity score, we have computed a mean of the scores by SNP weighted by the R2 between the SNP and the haplotype classification.

classifSNPsImpute is a version of classifSNPs that works with posterior probabilities of imputed genotypes.

List with the results:

scores: Matrix with the simmilarity scores of the individuals

numSNPs: Vector with the number of SNPs used in each computation

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