updated example data

phenotype_list.csv

@@ -9,16 +9,16 @@ FEV1/FVC ratio,fev1fvc,cont,l,0,10,sex,none,yes,ebi-a-GCST90029026
 Systolic blood pressure,sbp,cont,mmHg,0,250,sex:bp_med,none,yes,ukb-b-20175
 Diastolic blood pressure,dbp,cont,mmHg,0,250,sex:bp_med,none,yes,
 LDL cholesterol,ldl,cont,mmol/L,0,10,sex:cholesterol_med,none,yes,ieu-b-110
-HDL cholesterol,hdl,cont,mmol/L,0,10,sex,none,yes,ieu-b-109
-Triglycerides,trig,cont,mmol/L,0,20,sex,none,yes,ieu-b-111
+HDL cholesterol,hdl,cont,mmol/L,0,10,sex:cholesterol_med,none,yes,ieu-b-109
+Triglycerides,trig,cont,mmol/L,0,20,sex:cholesterol_med,none,yes,ieu-b-111
 C-reactive protein,crp,cont,mg/L,0,100,sex,none,yes,ebi-a-GCST90014002
 Interleukin 6,il6,cont,pg/ml,0,100,sex,none,yes,ebi-a-GCST90012005
 Leptin,leptin,cont,ng/ml,0,100,sex,none,yes,ebi-a-GCST90007307
-Glycated haemoglobin,hba1c,cont,mmol/mol,0,70,sex,none,yes,ebi-a-GCST90014006
-Insulin,insulin,cont,pmol/L,0,200,sex,none,yes,ukb-b-15445
+Glycated haemoglobin,hba1c,cont,mmol/mol,0,70,sex:insulin_med,none,yes,ebi-a-GCST90014006
+Insulin,insulin,cont,pmol/L,0,200,sex:insulin_med,none,yes,ukb-b-15445
 Adiponectin,adiponectin,cont,ug/ml,0,100,sex,none,yes,ieu-a-1
-Calcium,calcium,cont,mmol/L,0,10,sex,none,yes,ebi-a-GCST90013999
+Calcium,calcium,cont,mmol/L,0,10,sex:cholesterol_med,none,yes,ebi-a-GCST90013999
 Vitamin D,vitd,cont,nmol/L,0,400,sex,none,yes,ebi-a-GCST90000618
-Estradiol,estradiol,cont,pmol/L,0,15000,sex,none,yes,ebi-a-GCST90012105
-Testosterone,testosterone,cont,nmol/L,0,60,sex,none,yes,ebi-a-GCST90012114
-Sex hormone binding globulin,shbg,cont,nmol/L,0,300,sex,none,yes,ieu-b-4870
+Estradiol,estradiol,cont,pmol/L,0,15000,sex:hormone_med,none,yes,ebi-a-GCST90012105
+Testosterone,testosterone,cont,nmol/L,0,60,sex:hormone_med,none,yes,ebi-a-GCST90012114
+Sex hormone binding globulin,shbg,cont,nmol/L,0,300,sex:hormone_med,none,yes,ieu-b-4870

test/example-data/phen_input/adiponectin.txt

@@ -1,101 +1,31 @@
 FID	IID	value	age
-5258	5258	20.35	25.25
-2571	2571	60.36	73.08
-2600	2600	4.98	57.83
-8441	8441	69.29	60.08
-2973	2973	64.38	20.5
-4227	4227	74.88	50.83
-5180	5180	57.45	34.08
-7201	7201	80.98	70.5
-7941	7941	96.29	50.67
-6903	6903	84	79.92
-7973	7973	11.76	69.08
-8290	8290	75.9	41.92
-1110	1110	32.78	70.92
-3555	3555	89.45	33.5
-7514	7514	28.63	78.25
-8588	8588	9.99	21.83
-9697	9697	33.78	33.17
-5672	5672	87.2	75.58
-1697	1697	21.16	56
-1824	1824	54.47	58.83
-4544	4544	24.24	50.25
-9559	9559	33.04	40.92
-1458	1458	97.65	39.75
-1328	1328	43.48	39.08
-9473	9473	97.64	20.08
-4381	4381	98.26	38.58
-4957	4957	26.21	26.75
-5768	5768	17.74	62.92
-9295	9295	64.39	40.42
-3236	3236	8.66	66.33
-6958	6958	1.54	74.83
-9594	9594	4.11	28.17
-8956	8956	44.82	61.42
-7576	7576	74.53	51.67
-7980	7980	98.84	31.5
-5728	5728	53.86	59.92
-9675	9675	25.11	31.92
-6590	6590	67.34	24.75
-9794	9794	23.94	63.33
-2297	2297	29.44	63.92
-2008	2008	57.36	38.42
-7342	7342	43.4	77.25
-7162	7162	56.56	53.42
-9931	9931	65.65	22.75
-4331	4331	87.64	59.83
-3044	3044	42.6	20.92
-8002	8002	93.17	71.75
-4772	4772	54.03	26.42
-5939	5939	88.2	45
-3697	3697	56.67	63.83
-2443	2443	68.94	52.58
-7520	7520	93.22	46.83
-6766	6766	23.42	72.75
-2884	2884	40.9	46.5
-1164	1164	27.93	75.92
-3613	3613	83.93	27.25
-7889	7889	21.27	23.67
-9721	9721	39.44	63.58
-5851	5851	67.54	26.25
-7915	7915	17.37	52.67
-6345	6345	78.98	26.67
-3878	3878	38.07	47.17
-1880	1880	60.96	74.5
-6628	6628	37.9	49.33
-7849	7849	12.62	79.58
-1758	1758	60.99	47.25
-7625	7625	73.85	38.08
-1221	1221	99.4	23.33
-9939	9939	57.51	28
-2065	2065	26.09	54.08
-4925	4925	96.48	33.08
-8198	8198	30.93	30.92
-8325	8325	10.5	20.33
-4195	4195	77.35	21.42
-8883	8883	75.44	78.58
-2636	2636	23.57	29.5
-3516	3516	32.11	52.5
-6893	6893	67.2	46.42
-9385	9385	59.07	57.5
-6755	6755	33.59	78.5
-6989	6989	43.44	24.92
-3556	3556	94.76	39.42
-7671	7671	25.28	66.75
-4176	4176	12.28	65.83
-7774	7774	98.65	61.92
-7387	7387	95.53	57.75
-9235	9235	30.9	54.75
-6559	6559	47.52	58.67
-8756	8756	71.97	30.17
-9240	9240	38.55	69.67
-4763	4763	34.2	58.42
-8593	8593	35.1	24.5
-7081	7081	46.07	60.25
-6336	6336	41.11	64.5
-5991	5991	73.84	79.5
-2538	2538	21.26	48.25
-5158	5158	25.64	56.17
-3338	3338	50.04	28.42
-4062	4062	3.89	70.33
-9635	9635	47.93	46.17
+1122	1122	5.89	71.92
+1122	1122	15.58	66.92
+1187	1187	57.66	39.17
+2044	2044	38.08	54.83
+2044	2044	60.46	49.83
+2607	2607	99.39	45.67
+2607	2607	38.89	40.67
+2695	2695	8.09	68.67
+2900	2900	67.33	32.83
+3803	3803	77.62	67.42
+4998	4998	55.2	82.33
+4998	4998	21.55	77.33
+5038	5038	59.32	76.5
+5038	5038	7.01	71.5
+5244	5244	62.79	70.92
+5244	5244	54.86	65.92
+5372	5372	53.98	62.42
+5582	5582	5.95	55.08
+5582	5582	96.12	50.08
+6127	6127	78.61	59.92
+6127	6127	20.12	54.92
+7546	7546	72.25	52.17
+7613	7613	60.45	47.5
+7954	7954	38.07	24.5
+8083	8083	82.82	77.08
+8083	8083	39.84	72.08
+9211	9211	12.11	55.75
+9491	9491	72.13	30.75
+9685	9685	69.46	74.67
+9685	9685	79.05	69.67

test/example-data/phen_input/bmi.txt

@@ -1,101 +1,31 @@
 FID	IID	value	age
-5258	5258	39.7	25.25
-2571	2571	4.75	73.08
-2600	2600	53.47	57.83
-8441	8441	3.01	60.08
-2973	2973	34.94	20.5
-4227	4227	23.23	50.83
-5180	5180	31.82	34.08
-7201	7201	10.65	70.5
-7941	7941	27.41	50.67
-6903	6903	38.99	79.92
-7973	7973	21.12	69.08
-8290	8290	13.43	41.92
-1110	1110	20.41	70.92
-3555	3555	53.69	33.5
-7514	7514	41.37	78.25
-8588	8588	23.21	21.83
-9697	9697	3.49	33.17
-5672	5672	8.33	75.58
-1697	1697	24.12	56
-1824	1824	52.46	58.83
-4544	4544	12.22	50.25
-9559	9559	6.99	40.92
-1458	1458	51.23	39.75
-1328	1328	15.51	39.08
-9473	9473	1.45	20.08
-4381	4381	4.03	38.58
-4957	4957	23.74	26.75
-5768	5768	58.49	62.92
-9295	9295	10.06	40.42
-3236	3236	27.01	66.33
-6958	6958	1.59	74.83
-9594	9594	19.33	28.17
-8956	8956	46.32	61.42
-7576	7576	25.11	51.67
-7980	7980	37.28	31.5
-5728	5728	4.03	59.92
-9675	9675	44.77	31.92
-6590	6590	29.71	24.75
-9794	9794	43.93	63.33
-2297	2297	10.76	63.92
-2008	2008	16.18	38.42
-7342	7342	39.48	77.25
-7162	7162	42.9	53.42
-9931	9931	11.1	22.75
-4331	4331	29.7	59.83
-3044	3044	19.28	20.92
-8002	8002	19.23	71.75
-4772	4772	9.96	26.42
-5939	5939	57.4	45
-3697	3697	21.01	63.83
-2443	2443	59.49	52.58
-7520	7520	17.29	46.83
-6766	6766	27.32	72.75
-2884	2884	2.1	46.5
-1164	1164	2.82	75.92
-3613	3613	20.43	27.25
-7889	7889	45.27	23.67
-9721	9721	55.58	63.58
-5851	5851	23.59	26.25
-7915	7915	48.7	52.67
-6345	6345	7.38	26.67
-3878	3878	28.14	47.17
-1880	1880	53.62	74.5
-6628	6628	9.03	49.33
-7849	7849	7.14	79.58
-1758	1758	17.25	47.25
-7625	7625	55.45	38.08
-1221	1221	33.38	23.33
-9939	9939	44.06	28
-2065	2065	42.39	54.08
-4925	4925	3.48	33.08
-8198	8198	19.28	30.92
-8325	8325	59.13	20.33
-4195	4195	25.9	21.42
-8883	8883	14.01	78.58
-2636	2636	5.68	29.5
-3516	3516	21.39	52.5
-6893	6893	45.61	46.42
-9385	9385	6.07	57.5
-6755	6755	54.29	78.5
-6989	6989	38.71	24.92
-3556	3556	1.42	39.42
-7671	7671	58.29	66.75
-4176	4176	44.94	65.83
-7774	7774	26.1	61.92
-7387	7387	16.51	57.75
-9235	9235	20.23	54.75
-6559	6559	59.62	58.67
-8756	8756	54.82	30.17
-9240	9240	46.53	69.67
-4763	4763	52.17	58.42
-8593	8593	23.6	24.5
-7081	7081	26.21	60.25
-6336	6336	38.22	64.5
-5991	5991	38.13	79.5
-2538	2538	29.11	48.25
-5158	5158	41.44	56.17
-3338	3338	4.13	28.42
-4062	4062	26.42	70.33
-9635	9635	10.52	46.17
+1122	1122	26.08	71.92
+1122	1122	44.14	66.92
+1187	1187	31.71	39.17
+2044	2044	12.87	54.83
+2044	2044	50.52	49.83
+2607	2607	52.32	45.67
+2607	2607	32.43	40.67
+2695	2695	7.43	68.67
+2900	2900	46.7	32.83
+3803	3803	56.9	67.42
+4998	4998	13.47	82.33
+4998	4998	45.62	77.33
+5038	5038	40.44	76.5
+5038	5038	24.47	71.5
+5244	5244	20.95	70.92
+5244	5244	32.18	65.92
+5372	5372	29.56	62.42
+5582	5582	50.05	55.08
+5582	5582	1.54	50.08
+6127	6127	13.09	59.92
+6127	6127	50.42	54.92
+7546	7546	36.42	52.17
+7613	7613	47.44	47.5
+7954	7954	49.87	24.5
+8083	8083	44.77	77.08
+8083	8083	12.78	72.08
+9211	9211	44.99	55.75
+9491	9491	20.29	30.75
+9685	9685	45.46	74.67
+9685	9685	36.14	69.67