Commit 0d01bb24 authored by Philippe Veber's avatar Philippe Veber
Browse files

added in house LMM in pipeline

parent dc36ba8c
......@@ -4,11 +4,12 @@ let benchmark d =
let open Simulation_dataset in
Utils.recall_precision_curve
~oracle:(oracle d)
~labels:[|"topological";"multinomial";"gemma_score";"tdg09"|]
~labels:[|"topological";"multinomial";"gemma_score";"inhouse";"tdg09"|]
~results:[
topological d ;
multinomial_asymptotic_lrt d ;
gemma ~lmm_test:`Score ~relatedness_mode:`Standardized d ;
inhouse_lmm d ;
tdg09 d ;
]
......
......@@ -54,6 +54,8 @@ module type S = sig
relatedness_mode:[ `Centered | `Standardized ] ->
text file
val inhouse_lmm : query -> text file
val diffsel : query -> text file
val diffseldsparse :
......@@ -173,6 +175,11 @@ module Make (Q : Query) = struct
~relatedness_matrix
|> Gemma.result_table_of_output alignment
let inhouse_lmm q =
let alignment = amino_acid_alignment q in
let tree = tree ~branch_length_unit:`Amino_acid q in
Inhouse_lmm.test alignment tree
let diffseltree d =
Tree_dataset.prepare_diffsel_tree
(tree ~branch_length_unit:`Amino_acid d)
......
......@@ -54,6 +54,8 @@ module type S = sig
relatedness_mode:[ `Centered | `Standardized ] ->
text file
val inhouse_lmm : query -> text file
val diffsel : query -> text file
val diffseldsparse :
......
open Phylogenetics
open Codepitk
let%pworkflow[@version 2] test alignment tree =
let alignment =
Alignment.from_fasta [%path alignment]
|> Rresult.R.get_ok
in
let tree = Convergence_tree.from_file [%path tree] in
Inhouse_lmm.test ~alignment ~tree
|> Inhouse_lmm.result_table_of_test
|> Result_table.to_file ~output:[%dest]
open Bistro
open File_formats
val test :
aminoacid_fasta file ->
nhx file ->
text file
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