gemma.mli 811 Bytes
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open Bistro
open File_formats

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class type relatedness_matrix =
  object
    inherit text

    method format : [ `gemma_relatedness_matrix ]
  end
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val genotype_of_fasta : aminoacid_fasta file -> bimbam file
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val phenotype_of_tree : nhx file -> bimbam file
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val calculate_relatedness_matrix :
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  mode:[ `Centered | `Standardized ] ->
  genotype:bimbam file ->
  phenotype:bimbam file ->
  relatedness_matrix file

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class type univariate_lmm_output =
  object
    inherit tsv

    method format : [ `gemma_test_output ]
  end

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val univariate_lmm :
  lmm:[ `Wald | `LRT | `Score | `All ] ->
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  genotype:bimbam file ->
  phenotype:bimbam file ->
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  relatedness_matrix:relatedness_matrix file ->
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  univariate_lmm_output file
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val result_table_of_output :
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  aminoacid_fasta file -> univariate_lmm_output file -> cpt file