genal-python 0.5__tar.gz → 0.7__tar.gz

{genal_python-0.5 → genal_python-0.7}/.gitignore

@@ -2,4 +2,5 @@ __pycache__/
 dist/
 .ipynb_checkpoints/
 ipynb_checkpoints/
-genal/.ipynb_checkpoints/
+genal/.ipynb_checkpoints/
+docs/

{genal_python-0.5 → genal_python-0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: genal-python
-Version: 0.5
+Version: 0.7
 Summary: A python toolkit for polygenic risk scoring and mendelian randomization.
 Author-email: Cyprien Rivier <riviercyprien@gmail.com>
 Requires-Python: >=3.7
@@ -8,16 +8,19 @@ Description-Content-Type: text/markdown
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
 Classifier: Operating System :: OS Independent
-Requires-Dist: numpy>=1.26.2
+Requires-Dist: aiohttp==3.9.5
+Requires-Dist: nest_asyncio==1.5.5
+Requires-Dist: numpy>=1.24.4, <2.0
 Requires-Dist: pandas>=2.0.3
-Requires-Dist: plotnine>=0.12.3
-Requires-Dist: psutil>=5.9.1
-Requires-Dist: pyliftover>=0.4
+Requires-Dist: plotnine==0.12.3
+Requires-Dist: psutil==5.9.1
+Requires-Dist: pyliftover==0.4
 Requires-Dist: scikit_learn>=1.3.0
-Requires-Dist: scipy>=1.11.3
-Requires-Dist: statsmodels>=0.14.0
-Requires-Dist: tqdm>=4.66.1
-Requires-Dist: wget>=3.2
+Requires-Dist: scipy>=1.11.4
+Requires-Dist: sphinx_rtd_theme==1.3.0
+Requires-Dist: statsmodels==0.14.0
+Requires-Dist: tqdm==4.66.1
+Requires-Dist: wget==3.2
 Project-URL: Home, https://github.com/CypRiv/genal
 
 <center><h1> genal: A Python Toolkit for Genetic Risk Scoring and Mendelian Randomization </h1></center>
@@ -26,12 +29,14 @@ Project-URL: Home, https://github.com/CypRiv/genal
 
 **This project was developed by Cyprien A. Rivier**
 
+
 # Table of contents
 1. [Introduction](#introduction)
-2. [Requirements for the genal module](#paragraph1)
-3. [Installation and how to use genal](#paragraph2)
+2. [Citation] (#citation)
+3. [Requirements for the genal module](#paragraph1)
+4. [Installation and how to use genal](#paragraph2)
     1. [Installation](#paragraph2.1)
-4. [Tutorial and presentation of the main tools](#paragraph3)
+5. [Tutorial and presentation of the main tools](#paragraph3)
     1. [Data loading](#paragraph3.1)
     2. [Data preprocessing](#paragraph3.2)
     3. [Clumping](#paragraph3.3)
@@ -41,8 +46,6 @@ Project-URL: Home, https://github.com/CypRiv/genal
     7. [Lifting](#paragraph3.7)
 
 
-
-
 ## Introduction <a name="introduction"></a>
 Genal is a python module designed to make it easy to run genetic risk scores and mendelian randomization analyses. It integrates a collection of tools that facilitate the cleaning of single nucleotide polymorphism data (usually derived from Genome-Wide Association Studies) and enable the execution of clinical population genetic workflows. The functionalities provided by genal include clumping, lifting, association testing, polygenic risk scoring, and Mendelian randomization analyses, all within a single Python module.
 
@@ -50,6 +53,10 @@ The module prioritizes user-friendliness and intuitive operation, aiming to redu
 
 Genal draws on concepts from well-established R packages such as TwoSampleMR, MR-Presso, MendelianRandomization, and gwasvcf, adapting their proven methodologies to the Python environment. This approach ensures that users have access to tried and tested techniques with the versatility of Python's data science tools. 
 
+## Citation <a name="citation"></a> 
+If you're using genal, please cite the following paper:
+**Genal: A Python Toolkit for Genetic Risk Scoring and Mendelian Randomization.** Cyprien A. Rivier, Santiago Clocchiatti-Tuozzo, Shufan Huo, Victor Torres-Lopez, Daniela Renedo, Kevin N. Sheth, Guido J. Falcone, Julian N. Acosta. medRxiv 2024.05.23.24307776; doi: https://doi.org/10.1101/2024.05.23.24307776
+
 ## Requirements for the genal module <a name="paragraph1"></a> 
 ***Python 3.9 or later***. https://www.python.org/ <br> 
 
@@ -475,7 +482,7 @@ As expected, many MR methods indicate that SBP is strongly associated with strok
 To investigate horizontal pleiotropy in more details, a very useful method is Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO). MR-PRESSO is a method designed to detect and correct for horizontal pleiotropy. It will identify which instruments are likely to be pleiotropic on their effect on the outcome, and it will rerun an inverse-variance weighted MR after excluding them. It can be run using the `genal.Geno.MRpresso` method:
 
 ```python
-SBP_clumped.MRpresso(action = 2, n_iterations = 30000)
+mod_table, GlobalTest, OutlierTest, BiasTest = SBP_clumped.MRpresso(action = 2, n_iterations = 30000)
 ```
 
 As with the `genal.Geno.MR` method, the `action` argument determines how the pleiotropic SNPs will be treated. The output is a list containing:
@@ -520,7 +527,7 @@ At this point, genal will identify if the phenotype is binary or quantitative in
     Identified 0 as the control code in 'PHENO'. Set 'alternate_control=True' to inverse this interpretation.
     The phenotype data is stored in the .phenotype attribute.
     
-We can then run the association tests, specifying the path to the genetic files in plink format, and any columns we may want to include as covariates in the regression tests:
+We can then run the association tests, specifying the path to the genetic files in plink format, and any columns we may want to include as covariates in the regression tests (making sure that the covariates are all numerical):
 
 ```python
 SBP_adjusted.association_test(covar=["age"], path = "path/to/genetic/files")

{genal_python-0.5 → genal_python-0.7}/README.md

@@ -4,12 +4,14 @@
 
 **This project was developed by Cyprien A. Rivier**
 
+
 # Table of contents
 1. [Introduction](#introduction)
-2. [Requirements for the genal module](#paragraph1)
-3. [Installation and how to use genal](#paragraph2)
+2. [Citation] (#citation)
+3. [Requirements for the genal module](#paragraph1)
+4. [Installation and how to use genal](#paragraph2)
     1. [Installation](#paragraph2.1)
-4. [Tutorial and presentation of the main tools](#paragraph3)
+5. [Tutorial and presentation of the main tools](#paragraph3)
     1. [Data loading](#paragraph3.1)
     2. [Data preprocessing](#paragraph3.2)
     3. [Clumping](#paragraph3.3)
@@ -19,8 +21,6 @@
     7. [Lifting](#paragraph3.7)
 
 
-
-
 ## Introduction <a name="introduction"></a>
 Genal is a python module designed to make it easy to run genetic risk scores and mendelian randomization analyses. It integrates a collection of tools that facilitate the cleaning of single nucleotide polymorphism data (usually derived from Genome-Wide Association Studies) and enable the execution of clinical population genetic workflows. The functionalities provided by genal include clumping, lifting, association testing, polygenic risk scoring, and Mendelian randomization analyses, all within a single Python module.
 
@@ -28,6 +28,10 @@ The module prioritizes user-friendliness and intuitive operation, aiming to redu
 
 Genal draws on concepts from well-established R packages such as TwoSampleMR, MR-Presso, MendelianRandomization, and gwasvcf, adapting their proven methodologies to the Python environment. This approach ensures that users have access to tried and tested techniques with the versatility of Python's data science tools. 
 
+## Citation <a name="citation"></a> 
+If you're using genal, please cite the following paper:
+**Genal: A Python Toolkit for Genetic Risk Scoring and Mendelian Randomization.** Cyprien A. Rivier, Santiago Clocchiatti-Tuozzo, Shufan Huo, Victor Torres-Lopez, Daniela Renedo, Kevin N. Sheth, Guido J. Falcone, Julian N. Acosta. medRxiv 2024.05.23.24307776; doi: https://doi.org/10.1101/2024.05.23.24307776
+
 ## Requirements for the genal module <a name="paragraph1"></a> 
 ***Python 3.9 or later***. https://www.python.org/ <br> 
 
@@ -453,7 +457,7 @@ As expected, many MR methods indicate that SBP is strongly associated with strok
 To investigate horizontal pleiotropy in more details, a very useful method is Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO). MR-PRESSO is a method designed to detect and correct for horizontal pleiotropy. It will identify which instruments are likely to be pleiotropic on their effect on the outcome, and it will rerun an inverse-variance weighted MR after excluding them. It can be run using the `genal.Geno.MRpresso` method:
 
 ```python
-SBP_clumped.MRpresso(action = 2, n_iterations = 30000)
+mod_table, GlobalTest, OutlierTest, BiasTest = SBP_clumped.MRpresso(action = 2, n_iterations = 30000)
 ```
 
 As with the `genal.Geno.MR` method, the `action` argument determines how the pleiotropic SNPs will be treated. The output is a list containing:
@@ -498,7 +502,7 @@ At this point, genal will identify if the phenotype is binary or quantitative in
     Identified 0 as the control code in 'PHENO'. Set 'alternate_control=True' to inverse this interpretation.
     The phenotype data is stored in the .phenotype attribute.
     
-We can then run the association tests, specifying the path to the genetic files in plink format, and any columns we may want to include as covariates in the regression tests:
+We can then run the association tests, specifying the path to the genetic files in plink format, and any columns we may want to include as covariates in the regression tests (making sure that the covariates are all numerical):
 
 ```python
 SBP_adjusted.association_test(covar=["age"], path = "path/to/genetic/files")

{genal_python-0.5 → genal_python-0.7}/docs/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 00247dbbead88a90278898e19ea351de
+config: f327128ef63678afda2847b68c505d0e
 tags: 645f666f9bcd5a90fca523b33c5a78b7

genal_python-0.7/docs/_build/html/_sources/index.rst.txt

@@ -0,0 +1,59 @@
+.. genal documentation master file, created by
+   sphinx-quickstart on Thu Sep 14 14:04:16 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+genal: A Python Toolkit for Genetic Risk Scoring and Mendelian Randomization
+============================================================================
+
+:Author: Cyprien Rivier
+:Date: |today|
+:Version: "0.5"
+
+Genal is a python module designed to make it easy to run genetic risk scores and mendelian randomization analyses. It integrates a collection of tools that facilitate the cleaning of single nucleotide polymorphism data (usually derived from Genome-Wide Association Studies) and enable the execution of key clinical population genetic workflows. The functionalities provided by genal include clumping, lifting, association testing, polygenic risk scoring, and Mendelian randomization analyses, all within a single Python module.
+
+The module prioritizes user-friendliness and intuitive operation, aiming to reduce the complexity of data analysis for researchers. Despite its focus on simplicity, Genal does not sacrifice the depth of customization or the precision of analysis. Researchers can expect to maintain analytical rigour while benefiting from the streamlined experience.
+
+Genal draws on concepts from well-established R packages such as TwoSampleMR, MR-Presso, MendelianRandomization, and gwasvcf, adapting their proven methodologies to the Python environment. This approach ensures that users have access to tried and tested techniques with the versatility of Python's data science tools. 
+
+To install the latest release, type::
+
+    pip install genal
+
+Contents
+--------
+
+.. toctree::
+   :maxdepth: 2
+   
+   introduction.rst
+   api.rst
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+
+References
+----------
+
+.. [Hemani.2018] *The MR-Base platform supports systematic causal inference across the human phenome.*
+   Hemani G, Zheng J, Elsworth B, Wade KH, Baird D, Haberland V, Laurin C, Burgess S, Bowden J, Langdon R, Tan VY, Yarmolinsky J, Shihab HA, Timpson NJ, Evans DM, Relton C, Martin RM, Davey Smith G, Gaunt TR, Haycock PC, The MR-Base Collaboration
+   eLife. 2018 May 30:7:e34408 `34408 <https://elifesciences.org/articles/34408>`_.
+   PMID: `29846171 <https://pubmed.ncbi.nlm.nih.gov/29846171>`_.
+
+.. [Verbanck.2018] *Detection of widespread horizontal pleiotropy in causal relationships inferred from Mendelian randomization between complex traits and diseases.*
+   Marie Verbanck, Chia-Yen Chen, Benjamin Neale, Ron Do.
+   Nature Genetics 2018 May 50(5):693-698 `s41588-018-0099-7 <https://www.nature.com/articles/s41588-018-0099-7>`_.
+   PMID: `29686387 <https://pubmed.ncbi.nlm.nih.gov/29686387/>`_.
+
+.. [Lyon.2020] *The variant call format provides efficient and robust storage of GWAS summary statistics.*
+   Matthew Lyon, Shea J Andrews, Ben Elsworth, Tom R Gaunt, Gibran Hemani, Edoardo Marcora.
+   bioRxiv 2020 May 30 `2020.05.29.115824v1 <https://www.biorxiv.org/content/10.1101/2020.05.29.115824v1>`_.
+   PMID: `33441155 <https://pubmed.ncbi.nlm.nih.gov/33441155/>`_.
+