gwaslab 3.4.15__tar.gz → 3.4.16__tar.gz

{gwaslab-3.4.15/src/gwaslab.egg-info → gwaslab-3.4.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gwaslab
-Version: 3.4.15
+Version: 3.4.16
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/
@@ -32,7 +32,7 @@ Note: GWASLab is being updated very frequently for now. I will release the first
 ## Install
 
 ```
-pip install gwaslab==3.4.14
+pip install gwaslab==3.4.15
 ```
 
 

{gwaslab-3.4.15 → gwaslab-3.4.16}/README.md

@@ -18,7 +18,7 @@ Note: GWASLab is being updated very frequently for now. I will release the first
 ## Install
 
 ```
-pip install gwaslab==3.4.14
+pip install gwaslab==3.4.15
 ```
 
 

{gwaslab-3.4.15 → gwaslab-3.4.16}/pyproject.toml

@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "gwaslab"
-version = "3.4.15"
+version = "3.4.16"
 authors = [
   { name="Yunye", email="yunye@gwaslab.com" },
 ]

{gwaslab-3.4.15 → gwaslab-3.4.16}/src/gwaslab/__init__.py

@@ -32,4 +32,6 @@ from gwaslab.download import update_record
 from gwaslab.to_pickle import dump_pickle
 from gwaslab.to_pickle import load_pickle
 from gwaslab.config import options
-from gwaslab.version import _show_version as show_version
+from gwaslab.version import _show_version as show_version
+from gwaslab.calculate_power import get_power
+from gwaslab.calculate_power import get_beta

gwaslab-3.4.16/src/gwaslab/calculate_power.py

@@ -0,0 +1,124 @@
+import pandas as pd
+import numpy as np
+import scipy.stats as ss
+from gwaslab.Log import Log
+import scipy as sp
+
+def get_power(
+              mode="b",
+              t=0,
+              genotype_or=1.3 ,
+              beta=0.3,
+              eaf=0.1,
+              n=10000,
+              scase= 2000,
+              scontrol= 15000,
+              prevalence= 0.15,
+              daf = 0.2,
+              sig_level= 5e-8,
+              vary=1,
+              log=Log(),
+              verbose=True
+             ):
+    if mode=="b":
+        print("Input settings:{}".format(daf))
+        print(" -Number of cases:{}".format(scase))
+        print(" -Number of controls:{}".format(scontrol))
+        print(" -Risk allele OR:{:.3f}".format(genotype_or))
+        print(" -Disease prevalence:{:.3f}".format(prevalence))
+        print(" -Risk allele frequency: {:.3f}".format(daf))
+        print(" -Significance level: {:.3e}".format(sig_level))
+        # Skol, A. D., Scott, L. J., Abecasis, G. R., & Boehnke, M. (2006). Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nature genetics, 38(2), 209-213.
+        aaf = daf**2
+        abf = 2 * (daf) * (1 - daf)
+        bbf = (1- daf)**2
+
+        # additive
+        x = [ 2*genotype_or-1, genotype_or, 1 ] 
+
+        aap= x[0] * prevalence / (x[0]*aaf + x[1]*abf + x[2]*bbf)
+        abp= x[1] * prevalence / (x[0]*aaf + x[1]*abf + x[2]*bbf)
+        bbp= x[2] * prevalence / (x[0]*aaf + x[1]*abf + x[2]*bbf)
+        print("Probability of disease :")
+        print(" - Individuals with AA genotype: {:.3f}".format(aap))
+        print(" - Individuals with AB genotype: {:.3f}".format(abp))
+        print(" - Individuals with BB genotype: {:.3f}".format(bbp))
+        
+        pcase= (aap * aaf + abp * abf*0.5) / prevalence
+        pcontrol=((1-aap )* aaf + (1-abp )* abf*0.5) / (1 - prevalence)
+
+        vcase = pcase *(1-pcase)
+        vcontrol =pcontrol *(1-pcontrol)
+        print("Expected risk allele frequency:")
+        print(" - In cases: {:.3f}".format(pcase))
+        print(" - In controls: {:.3f}".format(pcontrol))
+
+        num= (pcase - pcontrol)
+        den= np.sqrt( (vcase/scase +  vcontrol/scontrol)*0.5 )
+        u = num / den
+
+        c = ss.norm.isf(sig_level/2)
+        power = 1 - ss.norm.cdf(c-u) + ss.norm.cdf(-c-u)
+        print("Expected power: {:.3f}".format(power))
+
+    elif mode=="q":
+        if verbose:
+            log.write("Significance level: {}".format(sig_level))
+            log.write("EAF: {}".format(eaf))
+            log.write("BETA: {}".format(beta))
+            log.write("N: {}".format(n))
+            log.write("H2: {}".format(2*eaf*(1-eaf)*(beta**2)))
+            c = ss.chi2.isf(sig_level/2,df=1)
+            NCP = n * 2*eaf*(1-eaf)*(beta**2)/vary
+            power = 1 - ss.ncx2.cdf(c,df=1,nc=NCP)
+
+    return power
+
+def get_beta(
+              mode="b",
+              t=0,
+              genotype_or=1.3 ,
+              eaf=0.1,
+              n=10000,
+              scase= 2000,
+              scontrol= 15000,
+              prevalence= 0.15,
+              daf = 0.2,
+              sig_level= 5e-8,
+              vary=1,
+              log=Log(),
+              verbose=True,
+              n_matrix=500
+             ):
+    if mode=="q":
+        if t >0:
+            def calculate_power_single(
+                                beta, 
+                                eaf, 
+                                n, 
+                                t, 
+                                sig_level=5e-8,vary=1):
+                
+                c = ss.chi2.isf(sig_level/2,df=1)
+                h2 = 2*eaf*(1-eaf)*(beta**2)
+                NCP = n * h2/vary
+                power = 1 - ss.ncx2.cdf(c,df=1,nc=NCP)
+                return power
+            
+            matrix = np.zeros((n_matrix,n_matrix),dtype=float)
+            eafs = np.linspace(0.5,0.0001,n_matrix)
+            betas =  np.linspace(0.0001,10,n_matrix)
+            
+            for i in range(n_matrix):
+                    matrix[i,] = calculate_power_single(beta=betas,eaf=eafs[i],n=n,t=t)
+            
+
+            i,j=1,1
+            eaf_beta = []
+            while i<n_matrix-1 and j<n_matrix-1:
+                if matrix[i,j] < t:
+                    j+=1
+                else:
+                    i+=1
+                    eaf_beta.append((eafs[i],betas[j]))
+        return pd.DataFrame(eaf_beta)

{gwaslab-3.4.15 → gwaslab-3.4.16}/src/gwaslab/mqqplot.py

@@ -322,7 +322,7 @@ def mqqplot(insumstats,
     
     # CHR and POS ########################################################################
     # chrom and pos exists && (m || r mode)
-    if (chrom is not None) and (pos is not None) and (("m" in mode) or ("r" in mode)):
+    if (chrom is not None) and (pos is not None) and (("qq" in mode) or ("m" in mode) or ("r" in mode)):
         # when manhattan plot, chrom and pos is needed.
         if chrom in insumstats.columns:
             usecols.append(chrom)

{gwaslab-3.4.15 → gwaslab-3.4.16/src/gwaslab.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: gwaslab
-Version: 3.4.15
+Version: 3.4.16
 Summary: A collection of handy tools for GWAS SumStats
 Author-email: Yunye <yunye@gwaslab.com>
 Project-URL: Homepage, https://cloufield.github.io/gwaslab/
@@ -32,7 +32,7 @@ Note: GWASLab is being updated very frequently for now. I will release the first
 ## Install
 
 ```
-pip install gwaslab==3.4.14
+pip install gwaslab==3.4.15
 ```
 
 

{gwaslab-3.4.15 → gwaslab-3.4.16}/src/gwaslab.egg-info/SOURCES.txt

@@ -38,6 +38,7 @@ src/gwaslab/rsID2chrpos.py
 src/gwaslab/textreposition.py
 src/gwaslab/to_formats.py
 src/gwaslab/to_pickle.py
+src/gwaslab/trumpetplot.py
 src/gwaslab/vchangestatus.py
 src/gwaslab/version.py
 src/gwaslab/winnerscurse.py

gwaslab-3.4.15/src/gwaslab/calculate_power.py

@@ -1,47 +0,0 @@
-def get_power(genotype_or=1.3 ,
-              scase= 2000,
-              scontrol= 15000,
-              prevalence= 0.15,
-              daf = 0.2,
-              sig_level= 5e-8
-             ):
-    print("Input settings:{}".format(daf))
-    print(" -Number of cases:{}".format(scase))
-    print(" -Number of controls:{}".format(scontrol))
-    print(" -Risk allele OR:{:.3f}".format(genotype_or))
-    print(" -Disease prevalence:{:.3f}".format(prevalence))
-    print(" -Risk allele frequency: {:.3f}".format(daf))
-    print(" -Significance level: {:.3e}".format(sig_level))
-    # Skol, A. D., Scott, L. J., Abecasis, G. R., & Boehnke, M. (2006). Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nature genetics, 38(2), 209-213.
-    aaf = daf**2
-    abf = 2 * (daf) * (1 - daf)
-    bbf = (1- daf)**2
-
-    # additive
-    x = [ 2*genotype_or-1, genotype_or, 1 ] 
-
-    aap= x[0] * prevalence / (x[0]*aaf + x[1]*abf + x[2]*bbf)
-    abp= x[1] * prevalence / (x[0]*aaf + x[1]*abf + x[2]*bbf)
-    bbp= x[2] * prevalence / (x[0]*aaf + x[1]*abf + x[2]*bbf)
-    print("Probability of disease :")
-    print(" - Individuals with AA genotype: {:.3f}".format(aap))
-    print(" - Individuals with AB genotype: {:.3f}".format(abp))
-    print(" - Individuals with BB genotype: {:.3f}".format(bbp))
-    
-    pcase= (aap * aaf + abp * abf*0.5) / prevalence
-    pcontrol=((1-aap )* aaf + (1-abp )* abf*0.5) / (1 - prevalence)
-
-    vcase = pcase *(1-pcase)
-    vcontrol =pcontrol *(1-pcontrol)
-    print("Expected risk allele frequency:")
-    print(" - In cases: {:.3f}".format(pcase))
-    print(" - In controls: {:.3f}".format(pcontrol))
-
-    num= (pcase - pcontrol)
-    den= np.sqrt( (vcase/scase +  vcontrol/scontrol)*0.5 )
-    u = num / den
-
-    c = ss.norm.isf(sig_level/2)
-    power = 1 - ss.norm.cdf(c-u) + ss.norm.cdf(-c-u)
-    print("Expected power: {:.3f}".format(power))
-    return power