This package contains a number of useful QTL mapping utilities. It supports single locus modeling in terms of haplotype descent and SNPs. These methods make use of a genome cache directory that contains information on haplotype descent for all individuals at all loci in a specific file setup. For haplotypes, both regression-on-probabilities (ROP) and multiple imputations are possible. For SNPs, dosages (imputation from haplotypes - in the human GWAS sense) are used. An invertible relationship matrix can be used to include a random effect. Exact and approximate (estimation of variance components only under the null model) anlysis are possible. For haplotype analysis, weights can be included on the error covariance matrix.
|License||GPL (>= 2)|
|Package repository||View on GitHub|
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