rm her, cli.rsst

limix · Apr 15, 2019 · e4f757c · e4f757c
1 parent 72956b1
commit e4f757c
Show file tree

Hide file tree

Showing 67 changed files with 643 additions and 115 deletions.
diff --git a/doc/Makefile b/doc/Makefile
@@ -26,4 +26,4 @@ clean: Makefile
 
 livehtml:
 	cd .. && python setup.py develop; cd doc
-	sphinx-autobuild -b html -r "(.*\.(raw|bz2|hdf5|jpg|csv|gz)|_generated/.*)" $(SPHINXOPTS) . $(BUILDDIR)/html
+	sphinx-autobuild -b html -r "(.*\.(raw|bz2|hdf5|jpg|csv|gz)|_generated/.*|api/.*|_build/.*)" $(SPHINXOPTS) . $(BUILDDIR)/html
diff --git a/doc/api.rst b/doc/api.rst
@@ -6,7 +6,7 @@ I/O module
 ==========
 
 .. autosummary::
-    :toctree: _generated/
+    :toctree: api/
 
     limix.io.bgen.read
     limix.io.bimbam.read_phenotype
@@ -20,7 +20,7 @@ Quality control
 ===============
 
 .. autosummary::
-    :toctree: _generated/
+    :toctree: api/
 
     limix.qc.boxcox
     limix.qc.compute_maf
@@ -38,7 +38,7 @@ Statistics
 ==========
 
 .. autosummary::
-    :toctree: _generated/
+    :toctree: api/
 
     limix.stats.allele_expectation
     limix.stats.allele_frequency
@@ -56,15 +56,23 @@ Heritability estimation
 =======================
 
 .. autosummary::
-    :toctree: _generated/
+    :toctree: api/
 
     limix.her.estimate
 
+Variance decomposition
+======================
+
+.. autosummary::
+    :toctree: api/
+
+    limix.vardec.VarDec
+
 Quantitative trait loci
 =======================
 
 .. autosummary::
-    :toctree: _generated/
+    :toctree: api/
 
     limix.qtl.scan
     limix.qtl.iscan
@@ -73,7 +81,7 @@ Plotting & Graphics
 ===================
 
 .. autosummary::
-    :toctree: _generated/
+    :toctree: api/
 
     limix.plot.box_aspect
     limix.plot.ConsensusCurve
@@ -89,25 +97,11 @@ Plotting & Graphics
     limix.plot.get_pyplot
     limix.plot.show
 
-Generalised Linear Mixed Models
-===============================
-
-.. autosummary::
-    :toctree: _generated/
-
-    limix.glmm.GLMMComposer.covariance_matrices
-    limix.glmm.GLMMComposer.decomp
-    limix.glmm.GLMMComposer.fit
-    limix.glmm.GLMMComposer.fixed_effects
-    limix.glmm.GLMMComposer.likname
-    limix.glmm.GLMMComposer.lml
-    limix.glmm.GLMMComposer.y
-
 Shell utilities
 ===============
 
 .. autosummary::
-    :toctree: _generated/
+    :toctree: api/
 
     limix.sh.filehash
     limix.sh.download

diff --git a/doc/api/limix.her.estimate.rst b/doc/api/limix.her.estimate.rst
@@ -0,0 +1,6 @@
+limix.her.estimate
+==================
+
+.. currentmodule:: limix.her
+
+.. autofunction:: estimate
diff --git a/doc/api/limix.io.bgen.read.rst b/doc/api/limix.io.bgen.read.rst
@@ -0,0 +1,6 @@
+limix.io.bgen.read
+==================
+
+.. currentmodule:: limix.io.bgen
+
+.. autofunction:: read
diff --git a/doc/api/limix.io.bimbam.read_phenotype.rst b/doc/api/limix.io.bimbam.read_phenotype.rst
@@ -0,0 +1,6 @@
+limix.io.bimbam.read\_phenotype
+===============================
+
+.. currentmodule:: limix.io.bimbam
+
+.. autofunction:: read_phenotype
diff --git a/doc/api/limix.io.csv.read.rst b/doc/api/limix.io.csv.read.rst
@@ -0,0 +1,6 @@
+limix.io.csv.read
+=================
+
+.. currentmodule:: limix.io.csv
+
+.. autofunction:: read
diff --git a/doc/api/limix.io.gen.read.rst b/doc/api/limix.io.gen.read.rst
@@ -0,0 +1,6 @@
+limix.io.gen.read
+=================
+
+.. currentmodule:: limix.io.gen
+
+.. autofunction:: read
diff --git a/doc/api/limix.io.hdf5.read_limix.rst b/doc/api/limix.io.hdf5.read_limix.rst
@@ -0,0 +1,6 @@
+limix.io.hdf5.read\_limix
+=========================
+
+.. currentmodule:: limix.io.hdf5
+
+.. autofunction:: read_limix
diff --git a/doc/api/limix.io.npy.read.rst b/doc/api/limix.io.npy.read.rst
@@ -0,0 +1,6 @@
+limix.io.npy.read
+=================
+
+.. currentmodule:: limix.io.npy
+
+.. autofunction:: read
diff --git a/doc/api/limix.io.plink.read.rst b/doc/api/limix.io.plink.read.rst
@@ -0,0 +1,6 @@
+limix.io.plink.read
+===================
+
+.. currentmodule:: limix.io.plink
+
+.. autofunction:: read
diff --git a/doc/api/limix.plot.ConsensusCurve.rst b/doc/api/limix.plot.ConsensusCurve.rst
@@ -0,0 +1,24 @@
+limix.plot.ConsensusCurve
+=========================
+
+.. currentmodule:: limix.plot
+
+.. autoclass:: ConsensusCurve
+
+
+   .. automethod:: __init__
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+      ~ConsensusCurve.__init__
+      ~ConsensusCurve.add
+      ~ConsensusCurve.consensus
+
+
+
+
+
+
diff --git a/doc/api/limix.plot.box_aspect.rst b/doc/api/limix.plot.box_aspect.rst
@@ -0,0 +1,6 @@
+limix.plot.box\_aspect
+======================
+
+.. currentmodule:: limix.plot
+
+.. autofunction:: box_aspect
diff --git a/doc/api/limix.plot.get_pyplot.rst b/doc/api/limix.plot.get_pyplot.rst
@@ -0,0 +1,6 @@
+limix.plot.get\_pyplot
+======================
+
+.. currentmodule:: limix.plot
+
+.. autofunction:: get_pyplot
diff --git a/doc/api/limix.plot.image.rst b/doc/api/limix.plot.image.rst
@@ -0,0 +1,6 @@
+limix.plot.image
+================
+
+.. currentmodule:: limix.plot
+
+.. autofunction:: image
diff --git a/doc/api/limix.plot.kinship.rst b/doc/api/limix.plot.kinship.rst
@@ -0,0 +1,6 @@
+limix.plot.kinship
+==================
+
+.. currentmodule:: limix.plot
+
+.. autofunction:: kinship
diff --git a/doc/api/limix.plot.load_dataset.rst b/doc/api/limix.plot.load_dataset.rst
@@ -0,0 +1,6 @@
+limix.plot.load\_dataset
+========================
+
+.. currentmodule:: limix.plot
+
+.. autofunction:: load_dataset
diff --git a/doc/api/limix.plot.manhattan.rst b/doc/api/limix.plot.manhattan.rst
@@ -0,0 +1,6 @@
+limix.plot.manhattan
+====================
+
+.. currentmodule:: limix.plot
+
+.. autofunction:: manhattan
diff --git a/doc/api/limix.plot.normal.rst b/doc/api/limix.plot.normal.rst
@@ -0,0 +1,6 @@
+limix.plot.normal
+=================
+
+.. currentmodule:: limix.plot
+
+.. autofunction:: normal
diff --git a/doc/api/limix.plot.pca.rst b/doc/api/limix.plot.pca.rst
@@ -0,0 +1,6 @@
+limix.plot.pca
+==============
+
+.. currentmodule:: limix.plot
+
+.. autofunction:: pca
diff --git a/doc/api/limix.plot.power.rst b/doc/api/limix.plot.power.rst
@@ -0,0 +1,6 @@
+limix.plot.power
+================
+
+.. currentmodule:: limix.plot
+
+.. autofunction:: power
diff --git a/doc/api/limix.plot.qqplot.rst b/doc/api/limix.plot.qqplot.rst
@@ -0,0 +1,6 @@
+limix.plot.qqplot
+=================
+
+.. currentmodule:: limix.plot
+
+.. autofunction:: qqplot
diff --git a/doc/api/limix.plot.show.rst b/doc/api/limix.plot.show.rst
@@ -0,0 +1,6 @@
+limix.plot.show
+===============
+
+.. currentmodule:: limix.plot
+
+.. autofunction:: show
diff --git a/doc/api/limix.qc.boxcox.rst b/doc/api/limix.qc.boxcox.rst
@@ -0,0 +1,6 @@
+limix.qc.boxcox
+===============
+
+.. currentmodule:: limix.qc
+
+.. autofunction:: boxcox
diff --git a/doc/api/limix.qc.compute_maf.rst b/doc/api/limix.qc.compute_maf.rst
@@ -0,0 +1,6 @@
+limix.qc.compute\_maf
+=====================
+
+.. currentmodule:: limix.qc
+
+.. autofunction:: compute_maf
diff --git a/doc/api/limix.qc.count_missingness.rst b/doc/api/limix.qc.count_missingness.rst
@@ -0,0 +1,6 @@
+limix.qc.count\_missingness
+===========================
+
+.. currentmodule:: limix.qc
+
+.. autofunction:: count_missingness
diff --git a/doc/api/limix.qc.indep_pairwise.rst b/doc/api/limix.qc.indep_pairwise.rst
@@ -0,0 +1,6 @@
+limix.qc.indep\_pairwise
+========================
+
+.. currentmodule:: limix.qc
+
+.. autofunction:: indep_pairwise
diff --git a/doc/api/limix.qc.mean_impute.rst b/doc/api/limix.qc.mean_impute.rst
@@ -0,0 +1,6 @@
+limix.qc.mean\_impute
+=====================
+
+.. currentmodule:: limix.qc
+
+.. autofunction:: mean_impute
diff --git a/doc/api/limix.qc.mean_standardize.rst b/doc/api/limix.qc.mean_standardize.rst
@@ -0,0 +1,6 @@
+limix.qc.mean\_standardize
+==========================
+
+.. currentmodule:: limix.qc
+
+.. autofunction:: mean_standardize
diff --git a/doc/api/limix.qc.normalise_covariance.rst b/doc/api/limix.qc.normalise_covariance.rst
@@ -0,0 +1,6 @@
+limix.qc.normalise\_covariance
+==============================
+
+.. currentmodule:: limix.qc
+
+.. autofunction:: normalise_covariance
diff --git a/doc/api/limix.qc.quantile_gaussianize.rst b/doc/api/limix.qc.quantile_gaussianize.rst
@@ -0,0 +1,6 @@
+limix.qc.quantile\_gaussianize
+==============================
+
+.. currentmodule:: limix.qc
+
+.. autofunction:: quantile_gaussianize
diff --git a/doc/api/limix.qc.regress_out.rst b/doc/api/limix.qc.regress_out.rst
@@ -0,0 +1,6 @@
+limix.qc.regress\_out
+=====================
+
+.. currentmodule:: limix.qc
+
+.. autofunction:: regress_out
diff --git a/doc/api/limix.qc.remove_dependent_cols.rst b/doc/api/limix.qc.remove_dependent_cols.rst
@@ -0,0 +1,6 @@
+limix.qc.remove\_dependent\_cols
+================================
+
+.. currentmodule:: limix.qc
+
+.. autofunction:: remove_dependent_cols
diff --git a/doc/api/limix.qc.unique_variants.rst b/doc/api/limix.qc.unique_variants.rst
@@ -0,0 +1,6 @@
+limix.qc.unique\_variants
+=========================
+
+.. currentmodule:: limix.qc
+
+.. autofunction:: unique_variants
diff --git a/doc/api/limix.qtl.iscan.rst b/doc/api/limix.qtl.iscan.rst
@@ -0,0 +1,6 @@
+limix.qtl.iscan
+===============
+
+.. currentmodule:: limix.qtl
+
+.. autofunction:: iscan
diff --git a/doc/api/limix.qtl.scan.rst b/doc/api/limix.qtl.scan.rst
@@ -0,0 +1,6 @@
+limix.qtl.scan
+==============
+
+.. currentmodule:: limix.qtl
+
+.. autofunction:: scan
diff --git a/doc/api/limix.sh.download.rst b/doc/api/limix.sh.download.rst
@@ -0,0 +1,6 @@
+limix.sh.download
+=================
+
+.. currentmodule:: limix.sh
+
+.. autofunction:: download
diff --git a/doc/api/limix.sh.extract.rst b/doc/api/limix.sh.extract.rst
@@ -0,0 +1,6 @@
+limix.sh.extract
+================
+
+.. currentmodule:: limix.sh
+
+.. autofunction:: extract