Commit 18a83e34 authored by Philippe Veber's avatar Philippe Veber
Browse files

app/lmm_benchmark: added inhouse tdg09

parent 0a6a31de
......@@ -61,6 +61,7 @@ let meth ?(requires_rooted_tree = false) f label =
let methods = Pipeline.[
meth tdg09 "tdg09" ;
meth inhouse_tdg09 "inhouse_tdg09" ;
(* meth pcoc "pcoc" ; *)
(* meth pcoc_v2 ~col:3 "pcoc v2" ; *)
meth (gemma ~lmm_test:`Score ~relatedness_mode:`Standardized) "gemma" ;
......@@ -99,9 +100,9 @@ let () =
(* module Top = Bistro_utils.Toplevel_eval.Make(struct
let np = 10
let mem = 8
let mem = 8
end)() *)
(*
(*
let () =
let q =
Pipeline.query ~seed:42 ~tree:(NHX besnard2009.tree) ~branch_scale:1. ~ne_s:(1., 1.)
......@@ -110,7 +111,7 @@ let () =
in
(* Gemma.calculate_relatedness_matrix
~mode:`Standardized
~genotype:(Gemma.genotype_of_fasta (Pipeline.amino_acid_alignment q))
~genotype:(Gemma.genotype_of_fasta (Pipeline.amino_acid_alignment q))
~phenotype:(Gemma.phenotype_of_tree (Pipeline.tree ~branch_length_unit:`Amino_acid q)) *)
Pipeline.lmm_with_gemma_matrix q ~relatedness_mode:`Standardized
|> Top.path
......
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