maradoner 0.14.3__tar.gz → 0.15.0__tar.gz

{maradoner-0.14.3 → maradoner-0.15.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: maradoner
-Version: 0.14.3
+Version: 0.15.0
 Summary: Variance-adjusted estimation of motif activities.
 Home-page: https://github.com/autosome-ru/maradoner
 Author: Georgy Meshcheryakov

{maradoner-0.14.3 → maradoner-0.15.0}/maradoner/__init__.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-__version__ = '0.14.3'
+__version__ = '0.15.0'
 import importlib
 
 

{maradoner-0.14.3 → maradoner-0.15.0}/maradoner/grn.py

@@ -122,7 +122,7 @@ def bayesian_fdr_control(p0, alpha=0.05):
     return discoveries, threshold
 
 def grn(project_name: str,  output: str, use_hdf=False, save_stat=True,
-        fdr_alpha=0.05, prior_h1=1/100):
+        fdr_alpha=0.05, prior_h1=1/100, include_mean: bool = True):
     data = read_init(project_name)
     fmt = data.fmt
     with openers[fmt](f'{project_name}.fit.{fmt}', 'rb') as f:
@@ -178,13 +178,16 @@ def grn(project_name: str,  output: str, use_hdf=False, save_stat=True,
         os.makedirs(folder_stat, exist_ok=True)
     os.makedirs(folder_belief, exist_ok=True)
     for sigma, nu, name, inds in zip(promvar.T[..., None], nus,  group_names, group_inds):
-        # if name != 'anconeus':
-        #     continue
         print(name)
         var = (B_hat * nu + sigma)
-        Y_ = Y[:, inds][..., None, :] + BM
-        # theta = U[:, inds][..., None, :] + BM
-        theta = B[..., None] * U[:, inds] + BM
+        
+        Y_ = Y[:, inds][..., None, :] 
+        theta = B[..., None] * U[:, inds] 
+        if include_mean:
+            Y_ = Y_ + BM
+            theta = theta + BM
+            
+        
         loglr = 2 * B * (Y_ * theta).sum(axis=-1) - B_pow * (theta ** 2).sum(axis=-1)
         del Y_
         del theta

{maradoner-0.14.3 → maradoner-0.15.0}/maradoner/main.py

@@ -320,12 +320,13 @@ def _grn(name: str = Argument(..., help='Project name'),
                                            ' comparable to the expression file size.'),
          hdf: bool = Option(True, help='Use HDF format instead of tar.gz files. Typically eats much less space'),
          stat: bool = Option(True, help='Save statistics alongside probabilities.'),
-         prior_h1: float = Option(1/10, help='Prior belief on the expected fraction of motifs active per promoter.')):
+         prior_h1: float = Option(1/10, help='Prior belief on the expected fraction of motifs active per promoter.'),
+         means: bool = Option(True, help='Include motif-specific means in both H_0 and H_1 models, otherwise only activities deviations are being tested.')):
     t0 = time()
     p = Progress(SpinnerColumn(speed=0.5), TextColumn("[progress.description]{task.description}"), transient=True)
     p.add_task(description="Building GRN...", total=None)
     p.start()
-    grn(name, output=folder, use_hdf=hdf, save_stat=stat, prior_h1=prior_h1)
+    grn(name, output=folder, use_hdf=hdf, save_stat=stat, prior_h1=prior_h1, include_mean=means)
     p.stop()
     dt = time() - t0
     rprint(f'[green][bold]✔️[/bold] Done![/green]\t time: {dt:.2f} s.')

{maradoner-0.14.3 → maradoner-0.15.0}/maradoner.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: maradoner
-Version: 0.14.3
+Version: 0.15.0
 Summary: Variance-adjusted estimation of motif activities.
 Home-page: https://github.com/autosome-ru/maradoner
 Author: Georgy Meshcheryakov