diff --git a/doc/source/get_predicted_gain.rst b/doc/source/get_predicted_gain.rst new file mode 100644 index 0000000000000000000000000000000000000000..9dea792471e07a2846adb7a73d92f8f0c14ea103 --- /dev/null +++ b/doc/source/get_predicted_gain.rst @@ -0,0 +1,39 @@ +Compute JASS power gain from the genetic architecture of traits +=============================================================== + +In a recent study :cite:`suzuki2023trait`, we explore how the genetic architecture of the set of traits (heritability, genetic covariance, heritability undetected by the univariate test, ...) can be predictive of statistical power gain of the multi-trait test. + + + +We implement an additional command line tool to give access our predictive model (the **jass predict-gain** command). +This command allows the to score swiftly a large number of traits combinations and to focus on set of traits the most promising for multi-trait testing. + +To work the inittable provided to the **jass predict-gain** command must contain the genetic covariance between traits. + + +.. code-block:: shell + + jass predict-gain --inittable-path inittable_curated_111_traits_20-03-2024.hdf5 --combination_path ./combination_example.tsv --gain-path predicted_gain.tsv + + +The second argument (--combination_path) is a path to a file containing the set of traits to be scored. + +.. csv-table:: Set of traits + :widths: 20, 70 + :header-rows: 1 + + GRP1,z_GIANT_HIP z_GLG_HDL z_GLG_LDL z_MAGIC_2HGLU-ADJBMI + GRP2,z_SPIRO-UKB_FVC z_SPIRO-UKB_FEV1 z_TAGC_ASTHMA + +When executed the command will created a report at --gain-path + +.. csv-table:: Predicted gain + :header-rows: 1 + + traits,k,avg_distance_cor,mean_gencov,avg_Neff,avg_h2,avg_perc_h2_diff_region,log10_mean_gencov,log10_avg_distance_cor,gain + ['z_SPIRO-UKB_FVC'; 'z_SPIRO-UKB_FEV1'; 'z_TAGC_ASTHMA'],0.1,0.1731946683845993,0.0637,0.3843393026739591,0.2785193310634847,0.7976315890930669,0.8139196701681637,0.8013809378674498,0.06428524764535551 + ['z_GIANT_HIP'; 'z_GLG_HDL'; 'z_GLG_LDL'; 'z_MAGIC_2HGLU-ADJBMI'],0.2,0.14899001074867035,0.01535,0.12076877719858631,0.22628198390356655,0.9055326131023057,0.6573854616675169,0.7879956172999502,-0.010766494024690904 + +The last column provide the predicted gain ("the higher the more promising"). Note that extrapoling on new data might give lesser performances than reported in :cite:`suzuki2023trait`. + +.. bibliography:: reference.bib \ No newline at end of file diff --git a/doc/source/index.rst b/doc/source/index.rst index 270f8c072ce9a715e642250b4daf5aa1b29772b3..87967f4a2da31ea34bc97b1035c41e2f138b0896 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -14,6 +14,7 @@ JASS documentation install data_import generating_joint_analysis + get_predicted_gain command_line_usage web_usage web_admin diff --git a/doc/source/reference.bib b/doc/source/reference.bib index 469a6903a53fa58d8e729b5e0d0e3b16c820968f..901b14a9691c75bac3e660837b9f99777a24a58a 100644 --- a/doc/source/reference.bib +++ b/doc/source/reference.bib @@ -20,6 +20,13 @@ publisher={Oxford University Press} } +@article{suzuki2023trait, + title={Trait selection strategy in multi-trait GWAS: Boosting SNPs discoverability}, + author={Suzuki, Yuka and M{\'e}nager, Herv{\'e} and Brancotte, Bryan and Vernet, Rapha{\"e}l and Nerin, Cyril and Boetto, Christophe and Auvergne, Antoine and Linhard, Christophe and Torchet, Rachel and Lechat, Pierre and others}, + journal={bioRxiv}, + year={2023}, + publisher={Cold Spring Harbor Laboratory Preprints} +} @article{Pasaniuc2014,