updated crp covariates

phenotype_list.csv

@@ -11,7 +11,7 @@ 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: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
+C-reactive protein,crp,cont,mg/L,0,100,sex:cholesterol_med,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:insulin_med,none,yes,ebi-a-GCST90014006

test/example-data/phen_input/adiponectin.txt

@@ -1,31 +1,31 @@
 FID	IID	value	age
-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
+1504	1504	95.35	62.25
+1504	1504	34.83	57.25
+1763	1763	22.92	75.08
+1900	1900	66.64	57.08
+1979	1979	49.64	27.17
+2077	2077	3.33	56.42
+3922	3922	52.49	40.92
+3922	3922	98.7	35.92
+4050	4050	20.93	22.08
+4110	4110	34.15	67.08
+4577	4577	72.78	47.67
+4577	4577	58.47	42.67
+4670	4670	72.4	30.75
+4670	4670	56.08	25.75
+4731	4731	7.6	69.08
+4731	4731	1.21	64.08
+5190	5190	35.47	42.25
+5190	5190	35.68	37.25
+5725	5725	3.42	41.17
+5725	5725	14.76	36.17
+6120	6120	32.14	23.67
+7094	7094	66.38	54.25
+7094	7094	59.32	49.25
+7296	7296	34.09	27.08
+7317	7317	99.55	67.17
+7317	7317	48.01	62.17
+7388	7388	4.51	51.08
+7388	7388	37.41	46.08
+7524	7524	8.37	35.75
+8061	8061	46.86	76.67

test/example-data/phen_input/bmi.txt

@@ -1,31 +1,31 @@
 FID	IID	value	age
-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
+1504	1504	36.45	62.25
+1504	1504	33.78	57.25
+1763	1763	15.78	75.08
+1900	1900	52.22	57.08
+1979	1979	10.17	27.17
+2077	2077	44.35	56.42
+3922	3922	26.97	40.92
+3922	3922	54.14	35.92
+4050	4050	20.48	22.08
+4110	4110	10.24	67.08
+4577	4577	55.19	47.67
+4577	4577	3.37	42.67
+4670	4670	31.09	30.75
+4670	4670	56.75	25.75
+4731	4731	52.49	69.08
+4731	4731	25.24	64.08
+5190	5190	21.67	42.25
+5190	5190	45.99	37.25
+5725	5725	0.34	41.17
+5725	5725	5.31	36.17
+6120	6120	45.72	23.67
+7094	7094	6.08	54.25
+7094	7094	46.22	49.25
+7296	7296	57.82	27.08
+7317	7317	10.95	67.17
+7317	7317	53.41	62.17
+7388	7388	49.39	51.08
+7388	7388	22.75	46.08
+7524	7524	45.32	35.75
+8061	8061	43.06	76.67

test/example-data/phen_input/calcium.txt

@@ -1,31 +1,31 @@
 FID	IID	value	age	cholesterol_med
-1122	1122	4.65	71.92	1
-1122	1122	2.51	66.92	0
-1187	1187	3.81	39.17	0
-2044	2044	9.83	54.83	0
-2044	2044	2.87	49.83	1
-2607	2607	8.61	45.67	1
-2607	2607	3.74	40.67	0
-2695	2695	4.57	68.67	1
-2900	2900	8.2	32.83	0
-3803	3803	9.71	67.42	0
-4998	4998	1.72	82.33	0
-4998	4998	5.06	77.33	1
-5038	5038	0.52	76.5	0
-5038	5038	3.97	71.5	0
-5244	5244	5.55	70.92	1
-5244	5244	1.76	65.92	0
-5372	5372	2.5	62.42	1
-5582	5582	5.66	55.08	1
-5582	5582	0.77	50.08	1
-6127	6127	4.23	59.92	0
-6127	6127	4.31	54.92	1
-7546	7546	9.51	52.17	1
-7613	7613	2.14	47.5	0
-7954	7954	6.31	24.5	1
-8083	8083	1.3	77.08	0
-8083	8083	5.93	72.08	1
-9211	9211	3.92	55.75	0
-9491	9491	8.74	30.75	1
-9685	9685	7.31	74.67	1
-9685	9685	5.17	69.67	1
+1504	1504	3.64	62.25	1
+1504	1504	4.24	57.25	0
+1763	1763	1.53	75.08	1
+1900	1900	2.46	57.08	0
+1979	1979	9.01	27.17	0
+2077	2077	8.22	56.42	0
+3922	3922	8.25	40.92	0
+3922	3922	3	35.92	1
+4050	4050	3.65	22.08	1
+4110	4110	1.88	67.08	1
+4577	4577	3.04	47.67	1
+4577	4577	4.72	42.67	0
+4670	4670	1.84	30.75	0
+4670	4670	6.8	25.75	1
+4731	4731	4.3	69.08	1
+4731	4731	4.21	64.08	1
+5190	5190	7.86	42.25	0
+5190	5190	6.34	37.25	0
+5725	5725	2.93	41.17	1
+5725	5725	8.95	36.17	1
+6120	6120	5.79	23.67	0
+7094	7094	7.85	54.25	0
+7094	7094	1.91	49.25	1
+7296	7296	4.4	27.08	1
+7317	7317	8.25	67.17	1
+7317	7317	2.05	62.17	1
+7388	7388	8.05	51.08	0
+7388	7388	9.21	46.08	0
+7524	7524	1.2	35.75	0
+8061	8061	7.67	76.67	1

test/example-data/phen_input/crp.txt

@@ -1,31 +1,31 @@
-FID	IID	value	age
-1122	1122	71.32	71.92
-1122	1122	72.04	66.92
-1187	1187	39.03	39.17
-2044	2044	40.94	54.83
-2044	2044	55.6	49.83
-2607	2607	14.28	45.67
-2607	2607	62.85	40.67
-2695	2695	38.23	68.67
-2900	2900	38.56	32.83
-3803	3803	48	67.42
-4998	4998	76.14	82.33
-4998	4998	85.52	77.33
-5038	5038	69.66	76.5
-5038	5038	88.11	71.5
-5244	5244	35.71	70.92
-5244	5244	74.66	65.92
-5372	5372	36.17	62.42
-5582	5582	51.24	55.08
-5582	5582	15.94	50.08
-6127	6127	77.69	59.92
-6127	6127	41.18	54.92
-7546	7546	30.73	52.17
-7613	7613	52.93	47.5
-7954	7954	49.43	24.5
-8083	8083	92.59	77.08
-8083	8083	72.58	72.08
-9211	9211	39.81	55.75
-9491	9491	97.62	30.75
-9685	9685	90.61	74.67
-9685	9685	70.71	69.67
+FID	IID	value	age	cholesterol_med
+1504	1504	41.35	62.25	1
+1504	1504	38.17	57.25	0
+1763	1763	38.81	75.08	0
+1900	1900	12.29	57.08	1
+1979	1979	85.32	27.17	1
+2077	2077	97.87	56.42	1
+3922	3922	15.78	40.92	0
+3922	3922	43.25	35.92	0
+4050	4050	21.6	22.08	0
+4110	4110	31.74	67.08	1
+4577	4577	95.62	47.67	0
+4577	4577	51.89	42.67	1
+4670	4670	17.97	30.75	0
+4670	4670	3.66	25.75	0
+4731	4731	72.22	69.08	0
+4731	4731	92.63	64.08	0
+5190	5190	62.08	42.25	0
+5190	5190	63.85	37.25	0
+5725	5725	41.01	41.17	1
+5725	5725	4.25	36.17	1
+6120	6120	16.86	23.67	0
+7094	7094	14.79	54.25	0
+7094	7094	78.44	49.25	1
+7296	7296	34.73	27.08	1
+7317	7317	24.29	67.17	1
+7317	7317	17.19	62.17	0
+7388	7388	96.33	51.08	0
+7388	7388	21.64	46.08	0
+7524	7524	65.32	35.75	0
+8061	8061	82.33	76.67	1

test/example-data/phen_input/dbp.txt

@@ -1,31 +1,31 @@
 FID	IID	value	age	bp_med
-1122	1122	141.07	71.92	1
-1122	1122	177.71	66.92	0
-1187	1187	170.34	39.17	1
-2044	2044	202.25	54.83	1
-2044	2044	234.48	49.83	1
-2607	2607	5.09	45.67	1
-2607	2607	22.92	40.67	1
-2695	2695	128.21	68.67	1
-2900	2900	227.73	32.83	1
-3803	3803	174.26	67.42	0
-4998	4998	125.23	82.33	0
-4998	4998	10.31	77.33	1
-5038	5038	26.44	76.5	0
-5038	5038	193.04	71.5	0
-5244	5244	100.7	70.92	1
-5244	5244	74.65	65.92	0
-5372	5372	212.75	62.42	0
-5582	5582	163.86	55.08	1
-5582	5582	48.66	50.08	0
-6127	6127	235.5	59.92	0
-6127	6127	235.37	54.92	1
-7546	7546	10.78	52.17	1
-7613	7613	228.1	47.5	0
-7954	7954	4.42	24.5	1
-8083	8083	141.16	77.08	1
-8083	8083	33.84	72.08	1
-9211	9211	63.38	55.75	0
-9491	9491	153.91	30.75	1
-9685	9685	38.72	74.67	1
-9685	9685	130.3	69.67	0
+1504	1504	84.6	62.25	0
+1504	1504	64.41	57.25	0
+1763	1763	153.28	75.08	1
+1900	1900	46.66	57.08	0
+1979	1979	130.16	27.17	0
+2077	2077	140.23	56.42	0
+3922	3922	55.36	40.92	0
+3922	3922	232	35.92	1
+4050	4050	77.04	22.08	1
+4110	4110	136.36	67.08	0
+4577	4577	31.56	47.67	0
+4577	4577	147.71	42.67	0
+4670	4670	245.25	30.75	1
+4670	4670	194.71	25.75	0
+4731	4731	40.29	69.08	1
+4731	4731	189.84	64.08	1
+5190	5190	222.08	42.25	1
+5190	5190	132.11	37.25	1
+5725	5725	143.37	41.17	1
+5725	5725	238.49	36.17	1
+6120	6120	130.66	23.67	0
+7094	7094	223.7	54.25	0
+7094	7094	144.71	49.25	0
+7296	7296	224.06	27.08	1
+7317	7317	66.46	67.17	0
+7317	7317	72.17	62.17	0
+7388	7388	3.86	51.08	0
+7388	7388	215.36	46.08	0
+7524	7524	174.01	35.75	1
+8061	8061	220.83	76.67	1

test/example-data/phen_input/estradiol.txt

@@ -1,31 +1,31 @@
 FID	IID	value	age	hormone_med
-1122	1122	2044.54	71.92	0
-1122	1122	8231.35	66.92	1
-1187	1187	8502.07	39.17	0
-2044	2044	11838.6	54.83	0
-2044	2044	14950.6	49.83	0
-2607	2607	11927.48	45.67	1
-2607	2607	4633.57	40.67	1
-2695	2695	3288.25	68.67	0
-2900	2900	6700.1	32.83	0
-3803	3803	4973.38	67.42	0
-4998	4998	311.94	82.33	1
-4998	4998	12820.74	77.33	1
-5038	5038	433.42	76.5	1
-5038	5038	9451.64	71.5	0
-5244	5244	5670.68	70.92	0
-5244	5244	4648.37	65.92	0
-5372	5372	7695.24	62.42	0
-5582	5582	8781.54	55.08	0
-5582	5582	1266.03	50.08	0
-6127	6127	8102.62	59.92	1
-6127	6127	4313.55	54.92	0
-7546	7546	7464.29	52.17	1
-7613	7613	1649.4	47.5	0
-7954	7954	13378.21	24.5	1
-8083	8083	10182.49	77.08	1
-8083	8083	14909.61	72.08	1
-9211	9211	13321.9	55.75	0
-9491	9491	4085.86	30.75	1
-9685	9685	1896.48	74.67	1
-9685	9685	67.13	69.67	1
+1504	1504	437.7	62.25	1
+1504	1504	6127.54	57.25	0
+1763	1763	7120.43	75.08	0
+1900	1900	5692.89	57.08	0
+1979	1979	11858.23	27.17	0
+2077	2077	275.6	56.42	1
+3922	3922	4418.55	40.92	1
+3922	3922	6229.5	35.92	0
+4050	4050	10210.51	22.08	0
+4110	4110	8983.63	67.08	1
+4577	4577	12805.32	47.67	1
+4577	4577	4964.53	42.67	1
+4670	4670	4201.74	30.75	1
+4670	4670	1628.57	25.75	1
+4731	4731	13571.77	69.08	1
+4731	4731	3351.82	64.08	1
+5190	5190	5549.88	42.25	0
+5190	5190	2902.55	37.25	0
+5725	5725	10036.01	41.17	0
+5725	5725	9154.09	36.17	1
+6120	6120	9659.57	23.67	0
+7094	7094	1957.1	54.25	0
+7094	7094	7202.15	49.25	1
+7296	7296	7932.86	27.08	1
+7317	7317	12249.43	67.17	0
+7317	7317	7315.52	62.17	1
+7388	7388	2247.74	51.08	1
+7388	7388	8609.67	46.08	1
+7524	7524	10187.48	35.75	1
+8061	8061	14198.43	76.67	1