Merge branch 'ar/gh451' into 'master'

refactor(dmr, regions): makes effect sizes exp - control.

See merge request machine-learning/modkit!291

Author: ArtRand

modkit-core/src/dmr/llr_model.rs

@@ -191,7 +191,7 @@ impl ModificationCounts {
         interval: DmrInterval,
     ) -> MkResult<Self> {
         let score = llk_ratio(&control_counts, &exp_counts)?;
-        let coh_res = cohen_h(&control_counts, &exp_counts);
+        let coh_res = cohen_h(&exp_counts, &control_counts);
         Ok(Self {
             control_counts,
             exp_counts,
@@ -249,7 +249,7 @@ impl ModificationCounts {
     }
 
     fn effect_size(&self) -> f32 {
-        self.control_counts.frac_modified() - self.exp_counts.frac_modified()
+        self.exp_counts.frac_modified() - self.control_counts.frac_modified()
     }
 }
 

tests/resources/test_output_chr20-2.bed

@@ -1,7 +1,7 @@
 #chrom	start	end	name	score	strand	a_counts	a_total	b_counts	b_total	a_mod_percentages	b_mod_percentages	a_pct_modified	b_pct_modified	effect_size	cohen_h	cohen_h_low	cohen_h_high
-chr20	9838623	9839213	CpG: 47	257.34514203447543	.	C:57	1777	C:601	2091	C:3.21	C:28.74	0.032076534	0.2874223	-0.25534576	-0.7715211567869047	0.708284253638713	0.8347580599350964
-chr20	10034962	10035266	CpG: 35	1.294227443419004	.	C:7	1513	C:14	1349	C:0.46	C:1.04	0.00462657	0.010378058	-0.0057514883	-0.0679566754086949	-0.00543680228264623	0.14135015310003604
-chr20	10172120	10172545	CpG: 35	5.013026381110649	.	C:43	1228	C:70	1088	C:3.50	C:6.43	0.035016287	0.06433824	-0.02932195	-0.13643116482308143	0.054828613466501475	0.21803371617966139
-chr20	10217487	10218336	CpG: 59	173.7819873154349	.	C:136	2337	C:482	1838	C:5.82	C:26.22	0.058194265	0.26224157	-0.2040473	-0.5879686471848853	0.5268640027632352	0.6490732916065354
-chr20	10433628	10434345	CpG: 71	-0.13968153023233754	.	C:31	2748	C:36	3733	C:1.13	C:0.96	0.0112809315	0.009643719	0.0016372129	0.016102959313509635	-0.033161275613487945	0.06536719424050721
-chr20	10671925	10674963	CpG: 255	6.355823977093678	.	C:67	9459	C:153	12862	C:0.71	C:1.19	0.0070832013	0.011895506	-0.0048123044	-0.05004497666410637	0.023497206482167955	0.07659274684604479
+chr20	9838623	9839213	CpG: 47	257.34514203447543	.	C:57	1777	C:601	2091	C:3.21	C:28.74	0.032076534	0.2874223	0.25534576	0.7715211567869047	0.708284253638713	0.8347580599350964
+chr20	10034962	10035266	CpG: 35	1.294227443419004	.	C:7	1513	C:14	1349	C:0.46	C:1.04	0.00462657	0.010378058	0.0057514883	0.0679566754086949	-0.00543680228264623	0.14135015310003604
+chr20	10172120	10172545	CpG: 35	5.013026381110649	.	C:43	1228	C:70	1088	C:3.50	C:6.43	0.035016287	0.06433824	0.02932195	0.13643116482308143	0.054828613466501475	0.21803371617966139
+chr20	10217487	10218336	CpG: 59	173.7819873154349	.	C:136	2337	C:482	1838	C:5.82	C:26.22	0.058194265	0.26224157	0.2040473	0.5879686471848853	0.5268640027632352	0.6490732916065354
+chr20	10433628	10434345	CpG: 71	-0.13968153023233754	.	C:31	2748	C:36	3733	C:1.13	C:0.96	0.0112809315	0.009643719	-0.0016372129	-0.016102959313509635	-0.033161275613487945	0.06536719424050721
+chr20	10671925	10674963	CpG: 255	6.355823977093678	.	C:67	9459	C:153	12862	C:0.71	C:1.19	0.0070832013	0.011895506	0.0048123044	0.05004497666410637	0.023497206482167955	0.07659274684604479