Merge pull request #31 from mancusolab/test_spectral

enhance documentation

docs/files.rst

@@ -102,12 +102,13 @@ For ``*.meta.cs.tsv``, it will row-bind the output for single-ancestry SuShiE di
 Full Credible Set with Alphas
 -----------------------------
 
-By specifying ``--alphas``, SuShiE outputs a ``*.alphas.tsv`` file that tracks all the SNPs' PIP, :math:`\alpha` (see :ref:`Model`), whether in the credible set across all :math:`L`.
+By specifying ``--alphas``, SuShiE outputs a ``*.alphas.tsv`` file that tracks all the SNPs' PIP, :math:`\alpha` (see :ref:`Model`), and purity across all :math:`L`.
 
 If ``--meta`` and ``--mega`` are specified (see definitions in :ref:`meta`), it will output ``*.meta.alphas.tsv`` and ``*.mega.alphas.tsv``, respectively, to track the information inferred by meta SuShiE and mega SuShiE.
 
 For ``*.meta.alphas.tsv``, it will row-bind the output for single-ancestry SuShiE differed by column ``ancestry``.
 
+
 .. list-table::
    :header-rows: 1
 
@@ -147,7 +148,7 @@ For ``*.meta.alphas.tsv``, it will row-bind the output for single-ancestry SuShi
      - Integer
      - 0, 1
      - The indicator whether the SNP is in the first credible set. Depending on ``--L``, it can have extra columns.
-    * - purity_l1
+   * - purity_l1
      - float
      - 0.634
      - The sample-size-weighted average purity across ancestries. To compare with the ``--purity``, it will decide the value in ``in_cs_l1``. Depending on ``--L``, it can have extra columns.
@@ -172,6 +173,7 @@ For ``*.meta.alphas.tsv``, it will row-bind the output for single-ancestry SuShi
      - sushie, mega, ancestry_1
      - The inference method for this credible set.
 
+
 .. _weightsfile:
 Prediction Weights
 ------------------

docs/version.rst

@@ -17,5 +17,5 @@ Version History
      - Update io.corr function so that report all the correlation results no matter cs is pruned or not.
    * - 0.13
      - Add ``--keep`` command to enable user to specify a file that contains the subjects ID SuShiE will perform on. Add  ``--ancestry_index`` command to enable user to specify a file that contains the ancestry index for fine-mapping. With this, user can input single phenotype, genotype, and covariate file that contains all the subjects across ancestries. Implement padding to increase inference time. Record elbo at each iteration and can access it in the ``infer.SuShiEResult`` object. The alphas table now outputs the average purity and KL divergence for each ``L``. Change ``--kl_threshold`` to ``--divergence``. Add ``--maf`` command to remove SNPs that less than minor allele frequency threshold within each ancestry. Add ``--max_select`` command to randomly select maximum number of SNPs to compute purity to avoid unnecessary memory spending. Add a QC function to remove duplicated SNPs.
-    * - 0.14
-      - Remove KL-Divergence pruning. Enhance command line appearance and improve the output files contents. Fix small bugs on multivariate KL.
+   * - 0.14
+     - Remove KL-Divergence pruning. Enhance command line appearance and improve the output files contents. Fix small bugs on multivariate KL.