genal-python 1.1__tar.gz → 1.2__tar.gz

{genal_python-1.1 → genal_python-1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: genal-python
-Version: 1.1
+Version: 1.2
 Summary: A python toolkit for polygenic risk scoring and mendelian randomization.
 Author-email: Cyprien Rivier <riviercyprien@gmail.com>
 Requires-Python: >=3.8
@@ -29,10 +29,6 @@ Project-URL: Home, https://github.com/CypRiv/genal
 <center><h1> genal: A Python Toolkit for Genetic Risk Scoring and Mendelian Randomization </h1></center>
 
 
-
-**This project was developed by Cyprien A. Rivier**
-
-
 # Table of contents
 1. [Introduction](#introduction)
 2. [Citation](#citation)
@@ -62,6 +58,7 @@ Genal draws on concepts from well-established R packages such as TwoSampleMR, MR
 
 Genal flowchart. Created in https://www.BioRender.com
 ## Citation <a name="citation"></a> 
+This project was developed by Cyprien A. Rivier.
 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.  
@@ -350,26 +347,7 @@ and the output is:
     7(0.455%) duplicated SNPs have been removed. Use keep_dups=True to keep them.
     Extracting SNPs for each chromosome...
     SNPs extracted for chr1.
-    SNPs extracted for chr2.
-    SNPs extracted for chr3.
-    SNPs extracted for chr4.
-    SNPs extracted for chr5.
-    SNPs extracted for chr6.
-    SNPs extracted for chr7.
-    SNPs extracted for chr8.
-    SNPs extracted for chr9.
-    SNPs extracted for chr10.
-    SNPs extracted for chr11.
-    SNPs extracted for chr12.
-    SNPs extracted for chr13.
-    SNPs extracted for chr14.
-    SNPs extracted for chr15.
-    SNPs extracted for chr16.
-    SNPs extracted for chr17.
-    SNPs extracted for chr18.
-    SNPs extracted for chr19.
-    SNPs extracted for chr20.
-    SNPs extracted for chr21.
+    ...
     SNPs extracted for chr22.
     Merging SNPs extracted from each chromosome...
     Created bed/bim/fam fileset with extracted SNPs: tmp_GENAL/4f4ce6a7_allchr
@@ -438,7 +416,6 @@ Genal will print how many SNPs were successfully found and extracted from the ou
     
 
 > **Note:**
->Here as well you have the option to use proxies for the instruments that are not present in the outcome data:
 >
 > Here as well you have the option to use proxies for the instruments that are not present in the outcome data:
 >
@@ -482,7 +459,7 @@ You can specify several arguments. We refer to the API for a full list, but the
 - `action = 2`: Uses effect allele frequencies to attempt to flip them (conservative, default)
 - `action = 3`: Removes all palindromic SNPs (very conservative)
 
-If you choose the option 2 or 3 (recommended), genal will print the list of palindromic SNPs that have been removed from the analysis.
+When choosing the option 2 or 3 (recommended), genal will print the list of palindromic SNPs that have been removed from the analysis.
 
 By default, only some MR methods (inverse-variance weighted, weighted median, Simple mode, MR-Egger) are going to be run. But if you wish to run a different set of MR methods, you can pass a list of strings to the `methods` argument. The possible strings are:
 - `IVW` for the classical Inverse-Variance Weighted method with random effects
@@ -499,7 +476,7 @@ By default, only some MR methods (inverse-variance weighted, weighted median, Si
 - `Weighted-mode` for the Weighted mode method
 - `all` to run all the above methods
 
-For more fine-tuning, such as settings for the number of boostrapping iterations, please refer to the API: [https://genal.readthedocs.io/en/latest/modules.html#id4](MR method).
+For more fine-tuning, such as settings for the number of boostrapping iterations, please refer to the API: [https://genal.readthedocs.io/en/latest/modules.html#id4] (MR method).
 
 If you want to visualize the obtained MR results, you can use the `genal.Geno.MR_plot` method that will plot each SNP in an `effect_on_exposure x effect_on_outcome` plane as well as lines corresponding to different MR methods:
 
@@ -508,9 +485,9 @@ SBP_clumped.MR_plot(filename="MR_plot_SBP_AS")
 ```
 
 ![MR plot](docs/build/_images/MR_plot_SBP_AS.png)
-You can select which MR methods you wish to plot with the `methods` argument. Note that for an MR method to be plotted, they must be included in the latest `genal.Geno.MR` call of this `genal.Geno` instance.
+You can select which MR methods to plot with the `methods` argument. Note that for an MR method to be plotted, they must be included in the latest `genal.Geno.MR` call of this `genal.Geno` instance.
 
-If you wish to include the heterogeneity values (Cochran's Q) in the results, you can use the heterogeneity argument in the `genal.Geno.MR` call. Here, the heterogeneity for the inverse-variance weighted method:
+To include the heterogeneity values (Cochran's Q) in the results, you can use the heterogeneity argument in the `genal.Geno.MR` call. Here, the heterogeneity for the inverse-variance weighted method:
 
 ```python
 SBP_clumped.MR(action = 2, methods = ["Egger","IVW"], exposure_name = "SBP", outcome_name = "Stroke_eur", heterogeneity = True)
@@ -523,7 +500,7 @@ And that will give:
 | SBP      | Stroke_eur | Egger Intercept          | 1499 | -0.001381 | 0.000813  | 8.935529e-02  | 2959.965136 | 1497 | 1.253763e-98 |
 | SBP      | Stroke_eur | Inverse-Variance Weighted| 1499 | 0.023049  | 0.001061  | 1.382645e-104 | 2965.678836 | 1498 | 4.280737e-99 |
     
-If you wish to display the coefficients as odds ratios with confidence intervals for a binary outcome trait, you can use the `odds = True` argument:
+To display the coefficients as odds ratios with confidence intervals for a binary outcome trait, you can use the `odds = True` argument:
 
 ```python
 SBP_clumped.MR(action = 2, methods = ["Egger","IVW"], exposure_name = "SBP", outcome_name = "Stroke_eur", heterogeneity = True, odds = True)
@@ -589,26 +566,7 @@ Genal will print information regarding the number of individuals used in the tes
     CHR/POS columns present: SNPs searched based on genomic positions.
     Extracting SNPs for each chromosome...
     SNPs extracted for chr1.
-    SNPs extracted for chr2.
-    SNPs extracted for chr3.
-    SNPs extracted for chr4.
-    SNPs extracted for chr5.
-    SNPs extracted for chr6.
-    SNPs extracted for chr7.
-    SNPs extracted for chr8.
-    SNPs extracted for chr9.
-    SNPs extracted for chr10.
-    SNPs extracted for chr11.
-    SNPs extracted for chr12.
-    SNPs extracted for chr13.
-    SNPs extracted for chr14.
-    SNPs extracted for chr15.
-    SNPs extracted for chr16.
-    SNPs extracted for chr17.
-    SNPs extracted for chr18.
-    SNPs extracted for chr19.
-    SNPs extracted for chr20.
-    SNPs extracted for chr21.
+    ...
     SNPs extracted for chr22.
     Merging SNPs extracted from each chromosome...
     Created bed/bim/fam fileset with extracted SNPs: tmp_GENAL/e415aab3_allchr

{genal_python-1.1 → genal_python-1.2}/README.md

@@ -5,10 +5,6 @@
 <center><h1> genal: A Python Toolkit for Genetic Risk Scoring and Mendelian Randomization </h1></center>
 
 
-
-**This project was developed by Cyprien A. Rivier**
-
-
 # Table of contents
 1. [Introduction](#introduction)
 2. [Citation](#citation)
@@ -38,6 +34,7 @@ Genal draws on concepts from well-established R packages such as TwoSampleMR, MR
 
 Genal flowchart. Created in https://www.BioRender.com
 ## Citation <a name="citation"></a> 
+This project was developed by Cyprien A. Rivier.
 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.  
@@ -326,26 +323,7 @@ and the output is:
     7(0.455%) duplicated SNPs have been removed. Use keep_dups=True to keep them.
     Extracting SNPs for each chromosome...
     SNPs extracted for chr1.
-    SNPs extracted for chr2.
-    SNPs extracted for chr3.
-    SNPs extracted for chr4.
-    SNPs extracted for chr5.
-    SNPs extracted for chr6.
-    SNPs extracted for chr7.
-    SNPs extracted for chr8.
-    SNPs extracted for chr9.
-    SNPs extracted for chr10.
-    SNPs extracted for chr11.
-    SNPs extracted for chr12.
-    SNPs extracted for chr13.
-    SNPs extracted for chr14.
-    SNPs extracted for chr15.
-    SNPs extracted for chr16.
-    SNPs extracted for chr17.
-    SNPs extracted for chr18.
-    SNPs extracted for chr19.
-    SNPs extracted for chr20.
-    SNPs extracted for chr21.
+    ...
     SNPs extracted for chr22.
     Merging SNPs extracted from each chromosome...
     Created bed/bim/fam fileset with extracted SNPs: tmp_GENAL/4f4ce6a7_allchr
@@ -414,7 +392,6 @@ Genal will print how many SNPs were successfully found and extracted from the ou
     
 
 > **Note:**
->Here as well you have the option to use proxies for the instruments that are not present in the outcome data:
 >
 > Here as well you have the option to use proxies for the instruments that are not present in the outcome data:
 >
@@ -458,7 +435,7 @@ You can specify several arguments. We refer to the API for a full list, but the
 - `action = 2`: Uses effect allele frequencies to attempt to flip them (conservative, default)
 - `action = 3`: Removes all palindromic SNPs (very conservative)
 
-If you choose the option 2 or 3 (recommended), genal will print the list of palindromic SNPs that have been removed from the analysis.
+When choosing the option 2 or 3 (recommended), genal will print the list of palindromic SNPs that have been removed from the analysis.
 
 By default, only some MR methods (inverse-variance weighted, weighted median, Simple mode, MR-Egger) are going to be run. But if you wish to run a different set of MR methods, you can pass a list of strings to the `methods` argument. The possible strings are:
 - `IVW` for the classical Inverse-Variance Weighted method with random effects
@@ -475,7 +452,7 @@ By default, only some MR methods (inverse-variance weighted, weighted median, Si
 - `Weighted-mode` for the Weighted mode method
 - `all` to run all the above methods
 
-For more fine-tuning, such as settings for the number of boostrapping iterations, please refer to the API: [https://genal.readthedocs.io/en/latest/modules.html#id4](MR method).
+For more fine-tuning, such as settings for the number of boostrapping iterations, please refer to the API: [https://genal.readthedocs.io/en/latest/modules.html#id4] (MR method).
 
 If you want to visualize the obtained MR results, you can use the `genal.Geno.MR_plot` method that will plot each SNP in an `effect_on_exposure x effect_on_outcome` plane as well as lines corresponding to different MR methods:
 
@@ -484,9 +461,9 @@ SBP_clumped.MR_plot(filename="MR_plot_SBP_AS")
 ```
 
 ![MR plot](docs/build/_images/MR_plot_SBP_AS.png)
-You can select which MR methods you wish to plot with the `methods` argument. Note that for an MR method to be plotted, they must be included in the latest `genal.Geno.MR` call of this `genal.Geno` instance.
+You can select which MR methods to plot with the `methods` argument. Note that for an MR method to be plotted, they must be included in the latest `genal.Geno.MR` call of this `genal.Geno` instance.
 
-If you wish to include the heterogeneity values (Cochran's Q) in the results, you can use the heterogeneity argument in the `genal.Geno.MR` call. Here, the heterogeneity for the inverse-variance weighted method:
+To include the heterogeneity values (Cochran's Q) in the results, you can use the heterogeneity argument in the `genal.Geno.MR` call. Here, the heterogeneity for the inverse-variance weighted method:
 
 ```python
 SBP_clumped.MR(action = 2, methods = ["Egger","IVW"], exposure_name = "SBP", outcome_name = "Stroke_eur", heterogeneity = True)
@@ -499,7 +476,7 @@ And that will give:
 | SBP      | Stroke_eur | Egger Intercept          | 1499 | -0.001381 | 0.000813  | 8.935529e-02  | 2959.965136 | 1497 | 1.253763e-98 |
 | SBP      | Stroke_eur | Inverse-Variance Weighted| 1499 | 0.023049  | 0.001061  | 1.382645e-104 | 2965.678836 | 1498 | 4.280737e-99 |
     
-If you wish to display the coefficients as odds ratios with confidence intervals for a binary outcome trait, you can use the `odds = True` argument:
+To display the coefficients as odds ratios with confidence intervals for a binary outcome trait, you can use the `odds = True` argument:
 
 ```python
 SBP_clumped.MR(action = 2, methods = ["Egger","IVW"], exposure_name = "SBP", outcome_name = "Stroke_eur", heterogeneity = True, odds = True)
@@ -565,26 +542,7 @@ Genal will print information regarding the number of individuals used in the tes
     CHR/POS columns present: SNPs searched based on genomic positions.
     Extracting SNPs for each chromosome...
     SNPs extracted for chr1.
-    SNPs extracted for chr2.
-    SNPs extracted for chr3.
-    SNPs extracted for chr4.
-    SNPs extracted for chr5.
-    SNPs extracted for chr6.
-    SNPs extracted for chr7.
-    SNPs extracted for chr8.
-    SNPs extracted for chr9.
-    SNPs extracted for chr10.
-    SNPs extracted for chr11.
-    SNPs extracted for chr12.
-    SNPs extracted for chr13.
-    SNPs extracted for chr14.
-    SNPs extracted for chr15.
-    SNPs extracted for chr16.
-    SNPs extracted for chr17.
-    SNPs extracted for chr18.
-    SNPs extracted for chr19.
-    SNPs extracted for chr20.
-    SNPs extracted for chr21.
+    ...
     SNPs extracted for chr22.
     Merging SNPs extracted from each chromosome...
     Created bed/bim/fam fileset with extracted SNPs: tmp_GENAL/e415aab3_allchr

{genal_python-1.1 → genal_python-1.2}/docs/source/index.rst

@@ -12,7 +12,7 @@ genal: A Python Toolkit for Genetic Risk Scoring and Mendelian Randomization
 
 :Author: Cyprien A. Rivier
 :Date: |today|
-:Version: "1.0"
+:Version: "1.2"
 
 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.
 

{genal_python-1.1 → genal_python-1.2}/docs/source/introduction.rst

@@ -281,26 +281,7 @@ and the output is::
     7(0.455%) duplicated SNPs have been removed. Use keep_dups=True to keep them.
     Extracting SNPs for each chromosome...
     SNPs extracted for chr1.
-    SNPs extracted for chr2.
-    SNPs extracted for chr3.
-    SNPs extracted for chr4.
-    SNPs extracted for chr5.
-    SNPs extracted for chr6.
-    SNPs extracted for chr7.
-    SNPs extracted for chr8.
-    SNPs extracted for chr9.
-    SNPs extracted for chr10.
-    SNPs extracted for chr11.
-    SNPs extracted for chr12.
-    SNPs extracted for chr13.
-    SNPs extracted for chr14.
-    SNPs extracted for chr15.
-    SNPs extracted for chr16.
-    SNPs extracted for chr17.
-    SNPs extracted for chr18.
-    SNPs extracted for chr19.
-    SNPs extracted for chr20.
-    SNPs extracted for chr21.
+    ...
     SNPs extracted for chr22.
     Merging SNPs extracted from each chromosome...
     Created bed/bim/fam fileset with extracted SNPs: tmp_GENAL/4f4ce6a7_allchr
@@ -453,9 +434,9 @@ If you want to visualize the obtained MR results, you can use the :meth:`~genal.
 .. image:: Images/MR_plot_SBP_AS.png
    :alt: MR plot
 
-You can select which MR methods you wish to plot with the ``methods`` argument. Note that for an MR method to be plotted, they must be included in the latest :meth:`~genal.Geno.MR` call of this :class:`~genal.Geno` instance.
+You can select which MR methods to plot with the ``methods`` argument. Note that for an MR method to be plotted, they must be included in the latest :meth:`~genal.Geno.MR` call of this :class:`~genal.Geno` instance.
 
-If you wish to include the heterogeneity values (Cochran's Q) in the results, you can use the heterogeneity argument in the :meth:`~genal.Geno.MR` call. Here, the heterogeneity for the inverse-variance weighted method:
+To include the heterogeneity values (Cochran's Q) in the results, you can use the heterogeneity argument in the :meth:`~genal.Geno.MR` call. Here, the heterogeneity for the inverse-variance weighted method:
 
 .. code-block:: python
 
@@ -470,7 +451,7 @@ And that will give:
     1      SBP  Stroke_eur            Egger Intercept  1499 -0.001381  0.000813  8.935529e-02  2959.965136  1497  1.253763e-98
     2      SBP  Stroke_eur  Inverse-Variance Weighted  1499  0.023049  0.001061  1.382645e-104 2965.678836  1498  4.280737e-99
 
-If you wish to display the coefficients as odds ratios with confidence intervals for a binary outcome trait, you can use the `odds = True` argument:
+To display the coefficients as odds ratios with confidence intervals for a binary outcome trait, you can use the `odds = True` argument:
 
 .. code-block:: python
 
@@ -543,26 +524,7 @@ Genal will print information regarding the number of individuals used in the tes
     CHR/POS columns present: SNPs searched based on genomic positions.
     Extracting SNPs for each chromosome...
     SNPs extracted for chr1.
-    SNPs extracted for chr2.
-    SNPs extracted for chr3.
-    SNPs extracted for chr4.
-    SNPs extracted for chr5.
-    SNPs extracted for chr6.
-    SNPs extracted for chr7.
-    SNPs extracted for chr8.
-    SNPs extracted for chr9.
-    SNPs extracted for chr10.
-    SNPs extracted for chr11.
-    SNPs extracted for chr12.
-    SNPs extracted for chr13.
-    SNPs extracted for chr14.
-    SNPs extracted for chr15.
-    SNPs extracted for chr16.
-    SNPs extracted for chr17.
-    SNPs extracted for chr18.
-    SNPs extracted for chr19.
-    SNPs extracted for chr20.
-    SNPs extracted for chr21.
+    ...
     SNPs extracted for chr22.
     Merging SNPs extracted from each chromosome...
     Created bed/bim/fam fileset with extracted SNPs: tmp_GENAL/e415aab3_allchr