gwaslab 3.5.5__py3-none-any.whl → 3.5.7__py3-none-any.whl

gwaslab/__init__.py

@@ -47,4 +47,5 @@ from gwaslab.util_ex_run_susie import _run_susie_rss as run_susie_rss
 from gwaslab.io_read_tabular import _read_tabular as read_tabular
 from gwaslab.util_in_meta import meta_analyze
 from gwaslab.viz_plot_scatter_with_reg import scatter
-from gwaslab.util_in_fill_data import rank_based_int
+from gwaslab.util_in_fill_data import rank_based_int
+from gwaslab.g_SumstatsSet import SumstatsSet

gwaslab/g_Sumstats.py

@@ -30,6 +30,7 @@ from gwaslab.hm_harmonize_sumstats import rsidtochrpos
 from gwaslab.hm_harmonize_sumstats import parallelizeassignrsid
 from gwaslab.hm_harmonize_sumstats import parallelinferstrand
 from gwaslab.hm_harmonize_sumstats import parallelrsidtochrpos
+from gwaslab.hm_harmonize_sumstats import _paralleleinferafwithmaf
 from gwaslab.util_in_filter_value import filtervalues
 from gwaslab.util_in_filter_value import filterout
 from gwaslab.util_in_filter_value import filterin
@@ -39,6 +40,7 @@ from gwaslab.util_in_filter_value import _filter_indel
 from gwaslab.util_in_filter_value import _filter_palindromic
 from gwaslab.util_in_filter_value import _filter_snp
 from gwaslab.util_in_filter_value import _exclude_hla
+from gwaslab.util_in_filter_value import _search_variants
 from gwaslab.util_in_filter_value import inferbuild
 from gwaslab.util_in_filter_value import sampling
 from gwaslab.util_in_filter_value import _get_flanking
@@ -77,6 +79,7 @@ from gwaslab.util_ex_ldsc import _estimate_h2_by_ldsc
 from gwaslab.util_ex_ldsc import _estimate_rg_by_ldsc
 from gwaslab.util_ex_ldsc import _estimate_h2_cts_by_ldsc
 from gwaslab.util_ex_ldsc import _estimate_partitioned_h2_by_ldsc 
+from gwaslab.util_ex_ldproxyfinder import _extract_ld_proxy
 from gwaslab.bd_get_hapmap3 import gethapmap3
 from gwaslab.util_abf_finemapping import abf_finemapping
 from gwaslab.util_abf_finemapping import make_cs
@@ -590,6 +593,24 @@ class Sumstats():
         else:
             self.data = _exclude_hla(self.data,log=self.log,**kwargs)
 
+    def search(self, inplace=False, **kwargs):
+        if inplace is False:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = _search_variants(new_Sumstats_object.data,
+                                                        log=new_Sumstats_object.log,
+                                                        **kwargs)
+            return new_Sumstats_object
+        else:
+            self.data = _search_variants(self.data,log=self.log,**kwargs)
+    
+    def get_proxy(self,snplist, inplace=False, **kwargs):
+        if inplace is False:
+            new_Sumstats_object = copy.deepcopy(self)
+            new_Sumstats_object.data = _extract_ld_proxy(common_sumstats = new_Sumstats_object.data,
+                                                         snplist=snplist,
+                                                        log=new_Sumstats_object.log,
+                                                        **kwargs)
+            return new_Sumstats_object
 
     def random_variants(self,inplace=False,n=1,p=None,**kwargs):
         if inplace is True:
@@ -617,6 +638,11 @@ class Sumstats():
         self.data = paralleleinferaf(self.data,ref_infer=ref_infer,log=self.log,**kwargs)
         self.meta["gwaslab"]["references"]["ref_infer_af"] = ref_infer
         self.meta["gwaslab"]["references"]["ref_infer_af"] = _append_meta_record(self.meta["gwaslab"]["references"]["ref_infer_af"] , ref_infer)
+    def maf_to_eaf(self,ref_infer,**kwargs):
+        self.data = _paralleleinferafwithmaf(self.data,ref_infer=ref_infer,log=self.log,**kwargs)
+        self.meta["gwaslab"]["references"]["ref_infer_maf"] = ref_infer
+        self.meta["gwaslab"]["references"]["ref_infer_maf"] = _append_meta_record(self.meta["gwaslab"]["references"]["ref_infer_af"] , ref_infer)    
+    
     def plot_daf(self, **kwargs):
         fig,outliers = plotdaf(self.data, **kwargs)
         return fig, outliers
@@ -805,7 +831,7 @@ class Sumstats():
         credible_sets = make_cs(region_data,threshold=0.95,log=self.log)
         return region_data, credible_sets
     
-    
+
 ## LDSC ##############################################################################################
     def estimate_h2_by_ldsc(self, build=None, verbose=True, match_allele=True, how="right", **kwargs):
         if build is None: