Penalized estimation of haplotype frequencies
نویسندگان
چکیده
منابع مشابه
Haplotype Estimation from Fuzzy Genotypes Using Penalized Likelihood
The Composite Link Model is a generalization of the generalized linear model in which expected values of observed counts are constructed as a sum of generalized linear components. When combined with penalized likelihood, it provides a powerful and elegant way to estimate haplotype probabilities from observed genotypes. Uncertain ("fuzzy") genotypes, like those resulting from AFLP scores, can be...
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Recent literature has suggested that haplotype inference through close relatives, especially from nuclear families can be an alternative strategy in determining the linkage phase. In this paper, haplotype reconstruction and estimation of haplotype frequencies via expectation maximization (EM) algorithm including nuclear families with only one parent available is proposed. Parent and his (her) c...
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Variable selection via penalized estimation is appealing for dimension reduction. For penalized linear regression, Efron, et al. (2004) introduced the LARS algorithm. Recently, the coordinate descent (CD) algorithm was developed by Friedman, et al. (2007) for penalized linear regression and penalized logistic regression and was shown to gain computational superiority. This paper explores...
متن کاملHAPLOFREQ - Estimating Haplotype Frequencies E.ciently
A commonly used tool in disease association studies is the search for discrepancies between the haplotype distribution in the case and control populations. In order to find this discrepancy, the haplotypes frequency in each of the populations is estimated from the genotypes. We present a new method HAPLOFREQ to estimate haplotype frequencies over a short genomic region given the genotypes or ha...
متن کاملHAPLOFREQ - Estimating Haplotype Frequencies Efficiently
A commonly used tool in disease association studies is the search for discrepancies between the haplotype distribution in the case and control populations. In order to find this discrepancy, the haplotypes frequency in each of the populations is estimated from the genotypes. We present a new method HAPLOFREQ to estimate haplotype frequencies over a short genomic region given the genotypes or ha...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2008
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btn236