From 327579b297c0da4c76887d00f29a7e23d408f888 Mon Sep 17 00:00:00 2001 From: Andrea Raithel <133764907+andrearaithel@users.noreply.github.com> Date: Wed, 14 Aug 2024 14:56:39 +0200 Subject: [PATCH] Update prepare.rst to include useOHTtoObtainQ --- docs/source/prepare.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/source/prepare.rst b/docs/source/prepare.rst index 0bb67663..76231b12 100644 --- a/docs/source/prepare.rst +++ b/docs/source/prepare.rst @@ -107,6 +107,7 @@ padjCutoff numeric A number between (0, 1] indicating the maxTestedDimensionProportion numeric An integer that controls the maximum value that the encoding dimension can take. Refer to `advanced-options`_. ``3`` yieldSize numeric An integer that sets the batch size for counting reads within a bam file. If memory issues persist lower the yieldSize. ``2000000`` genesToTest character Full path to a yaml file specifying lists of candidate genes per sample to test during FDR correction. See the documentation for details on the structure of this file. ``/path/to/genes_to_test.yaml`` +useOHTtoObtainQ boolean If true, the optimal latent space dimension for the autoencoder will be determined by OHT. If false, a grid-search will be performed. ``true`` ============================ ========= ======================================================================================================================================================================= ====== Aberrant splicing dictionary @@ -138,6 +139,7 @@ deltaPsiCutoff numeric A non-negative number. Delta psi values padjCutoff numeric Same as in aberrant expression. ``0.1`` maxTestedDimensionProportion numeric Same as in aberrant expression. ``6`` genesToTest character Same as in aberrant expression. ``/path/to/genes_to_test.yaml`` +useOHTtoObtainQ boolean Same as in aberrant expression. ``true`` ============================ ========= ===================================================================================================================================================================================================================== ======