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admix-kit docs
admix-kit docs

Documentation

  • Overview
  • Dataset preparation
  • Command line interface
    • Association testing
    • Genetic correlation estimation
    • Local ancestry-specific polygenic score
    • Phenotype simulation
  • Python API
    • admix.assoc.marginal
    • admix.cli.admix_grm
    • admix.cli.admix_grm_merge
    • admix.cli.genet_cor
    • admix.data.calc_partial_pgs
    • admix.Dataset
    • admix.simulate.admix_geno
    • admix.simulate.quant_pheno
    • admix.simulate.binary_pheno
    • admix.simulate.quant_pheno_1pop
    • admix.simulate.quant_pheno_grm
    • admix.data.allele_per_anc
    • admix.data.af_per_anc
    • admix.io.read_dataset
    • admix.io.read_lanc
    • admix.io.read_rfmix
    • admix.tools.plink2.lift_over
    • admix.plot.lanc
    • admix.plot.admixture
    • admix.plot.manhattan
    • admix.plot.qq

Example usage

  • Admixed genotype simulation
  • Basic statistics and visualization
  • Association testing (GWAS)
  • Genetic correlation across local ancestry segments
  • Polygenic scoring for each local ancestry background
  • admix.Dataset
  • Selecting admixed individuals
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Command line interface#

We introduce the following main functions:

  • Association testing
  • Genetic correlation estimation
  • Local ancestry-specific polygenic score
  • Phenotype simulation
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Association testing
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Dataset preparation
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