BMI - Brain Caudate basal ganglia
sheng Qian
2021-2-6
Last updated: 2022-02-21
Checks: 6 1
Knit directory: cTWAS_analysis/
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Weight QC
#number of imputed weights
nrow(qclist_all)[1] 11538#number of imputed weights by chromosome
table(qclist_all$chr)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
1112 837 689 449 566 643 536 429 430 443 690 629 239 387 388 525
17 18 19 20 21 22
715 186 889 345 129 282 #number of imputed weights without missing variants
sum(qclist_all$nmiss==0)[1] 8973#proportion of imputed weights without missing variants
mean(qclist_all$nmiss==0)[1] 0.7777Check convergence of parameters
| Version | Author | Date |
|---|---|---|
| e6bc169 | sq-96 | 2022-02-13 |
#estimated group prior
estimated_group_prior <- group_prior_rec[,ncol(group_prior_rec)]
names(estimated_group_prior) <- c("gene", "snp")
estimated_group_prior["snp"] <- estimated_group_prior["snp"]*thin #adjust parameter to account for thin argument
print(estimated_group_prior) gene snp
0.0025716 0.0002996 #estimated group prior variance
estimated_group_prior_var <- group_prior_var_rec[,ncol(group_prior_var_rec)]
names(estimated_group_prior_var) <- c("gene", "snp")
print(estimated_group_prior_var) gene snp
18.14 17.47 #report sample size
print(sample_size)[1] 336107#report group size
group_size <- c(nrow(ctwas_gene_res), n_snps)
print(group_size)[1] 11538 7535010#estimated group PVE
estimated_group_pve <- estimated_group_prior_var*estimated_group_prior*group_size/sample_size #check PVE calculation
names(estimated_group_pve) <- c("gene", "snp")
print(estimated_group_pve) gene snp
0.001601 0.117318 #compare sum(PIP*mu2/sample_size) with above PVE calculation
c(sum(ctwas_gene_res$PVE),sum(ctwas_snp_res$PVE))[1] 0.2005 15.2164Genes with highest PIPs
genename region_tag susie_pip mu2 PVE z num_eqtl
4862 HEY2 6_84 1.0000 34549.60 1.028e-01 5.034 1
8605 MRPL1 4_52 1.0000 16661.36 4.957e-02 3.486 1
1577 ASCC2 22_10 0.9937 9364.23 2.769e-02 -2.618 1
3408 CCND2 12_4 0.8929 28.66 7.615e-05 -5.120 1
10379 SP1 12_33 0.7523 25.56 5.721e-05 -4.719 1
12572 ETV5 3_114 0.6941 94.99 1.962e-04 9.862 1
5598 C18orf8 18_12 0.6056 55.44 9.990e-05 7.500 2
13830 HIST1H2BE 6_20 0.4701 30.75 4.300e-05 -6.515 1
13559 CTC-498M16.4 5_52 0.4675 53.75 7.476e-05 7.706 1
6002 ECE2 3_113 0.4447 29.33 3.881e-05 -5.302 1
10039 KCNB2 8_53 0.4401 64.90 8.499e-05 -8.226 1
1258 KIF16B 20_12 0.4271 24.80 3.152e-05 -4.620 1
12886 AP006621.5 11_1 0.4133 25.01 3.075e-05 -4.506 1
7888 YWHAZ 8_69 0.3637 24.52 2.653e-05 4.235 1
8734 ELP5 17_6 0.3633 34.12 3.688e-05 4.157 2
1722 DNAJC5 20_38 0.3632 23.95 2.588e-05 -4.018 1
5697 IGLON5 19_35 0.3604 31.09 3.334e-05 -5.403 1
1031 IGSF9B 11_83 0.3492 29.78 3.094e-05 2.128 1
5546 CDH13 16_46 0.3484 24.86 2.577e-05 -4.826 1
11928 HRAT92 7_1 0.3484 31.53 3.268e-05 -3.948 3Genes with largest effect sizes
genename region_tag susie_pip mu2 PVE z num_eqtl
7909 CCDC171 9_13 0.0000000 51333 0.000e+00 7.979 1
4862 HEY2 6_84 1.0000000 34550 1.028e-01 5.034 1
9691 STX19 3_59 0.0000000 30626 0.000e+00 -5.060 1
10446 GSAP 7_49 0.0000000 30471 0.000e+00 5.260 1
13068 RP11-490G2.2 1_60 0.0000000 30364 0.000e+00 5.044 1
8151 LEO1 15_21 0.0005517 27533 4.519e-05 4.603 1
5468 MFAP1 15_16 0.0000000 23396 0.000e+00 4.303 1
4567 IGHMBP2 11_38 0.0000000 22373 0.000e+00 -4.328 2
13777 LINC02019 3_35 0.1023540 22219 6.766e-03 -4.490 1
5290 TMOD3 15_21 0.0000000 21923 0.000e+00 -5.412 1
11916 CKMT1A 15_16 0.0000000 21583 0.000e+00 -4.115 1
1364 WDR76 15_16 0.0000000 21090 0.000e+00 4.775 2
2991 CISH 3_35 0.0000000 19958 0.000e+00 -3.799 1
1222 C3orf18 3_35 0.0000000 18831 0.000e+00 4.682 1
2990 HEMK1 3_35 0.0000000 18831 0.000e+00 -4.682 1
3137 PLCL1 2_117 0.0000000 18556 0.000e+00 5.642 1
1064 CCNT2 2_80 0.0372469 18352 2.034e-03 3.686 1
2179 PDE4C 19_14 0.0000000 18026 0.000e+00 6.594 1
8605 MRPL1 4_52 0.9999963 16661 4.957e-02 3.486 1
5185 TUBGCP4 15_16 0.0000000 16113 0.000e+00 3.550 2Genes with highest PVE
genename region_tag susie_pip mu2 PVE z num_eqtl
4862 HEY2 6_84 1.0000000 34549.60 1.028e-01 5.034 1
8605 MRPL1 4_52 0.9999963 16661.36 4.957e-02 3.486 1
1577 ASCC2 22_10 0.9936907 9364.23 2.769e-02 -2.618 1
13777 LINC02019 3_35 0.1023540 22218.87 6.766e-03 -4.490 1
3071 LANCL1 2_124 0.2678433 4621.81 3.683e-03 -3.535 1
1064 CCNT2 2_80 0.0372469 18352.47 2.034e-03 3.686 1
7733 MFSD8 4_84 0.0539407 6711.44 1.077e-03 2.512 1
12572 ETV5 3_114 0.6940969 94.99 1.962e-04 9.862 1
10923 TTC30B 2_107 0.0714653 738.10 1.569e-04 -3.137 1
11912 VPS52 6_28 0.3349314 122.68 1.223e-04 1.606 1
5598 C18orf8 18_12 0.6056280 55.44 9.990e-05 7.500 2
10039 KCNB2 8_53 0.4401104 64.90 8.499e-05 -8.226 1
3408 CCND2 12_4 0.8929292 28.66 7.615e-05 -5.120 1
13559 CTC-498M16.4 5_52 0.4675212 53.75 7.476e-05 7.706 1
179 NISCH 3_36 0.1199919 169.37 6.047e-05 4.468 2
6862 GPR61 1_67 0.2539107 78.14 5.903e-05 8.755 1
10379 SP1 12_33 0.7523004 25.56 5.721e-05 -4.719 1
8151 LEO1 15_21 0.0005517 27533.18 4.519e-05 4.603 1
13830 HIST1H2BE 6_20 0.4700979 30.75 4.300e-05 -6.515 1
6002 ECE2 3_113 0.4447126 29.33 3.881e-05 -5.302 1Genes with largest z scores
genename region_tag susie_pip mu2 PVE z num_eqtl
7736 MST1R 3_35 2.778e-03 1066.54 8.816e-06 -12.646 3
38 RBM6 3_35 3.659e-04 898.10 9.778e-07 12.536 1
9298 KCTD13 16_24 3.260e-02 111.57 1.082e-05 11.491 1
5215 ADCY3 2_16 5.213e-05 181.06 2.808e-08 10.987 2
7732 RNF123 3_35 4.332e-12 814.77 1.050e-14 -10.959 1
1846 MAPK3 16_24 6.198e-03 99.06 1.827e-06 10.880 1
8639 INO80E 16_24 7.196e-03 95.02 2.034e-06 10.734 1
12763 RP11-1348G14.4 16_23 7.270e-02 92.18 1.994e-05 10.676 1
11175 NPIPB6 16_23 6.407e-02 94.15 1.795e-05 -10.506 1
10711 CLN3 16_23 3.079e-02 89.34 8.184e-06 10.453 1
9418 NUPR1 16_23 7.178e-02 98.60 2.106e-05 -10.437 2
9502 NFATC2IP 16_23 2.729e-02 87.47 7.102e-06 -10.013 1
8296 ZNF668 16_24 3.291e-02 78.13 7.649e-06 10.000 1
8995 C1QTNF4 11_29 7.823e-03 95.03 2.212e-06 9.961 2
12572 ETV5 3_114 6.941e-01 94.99 1.962e-04 9.862 1
1938 KAT8 16_24 6.258e-03 74.20 1.381e-06 -9.848 1
11718 NDUFS3 11_29 4.101e-03 85.99 1.049e-06 -9.624 1
11003 SULT1A2 16_23 8.563e-03 77.50 1.975e-06 -9.621 2
11724 LAT 16_23 5.360e-02 86.34 1.377e-05 -9.553 1
2577 MTCH2 11_29 3.824e-03 84.27 9.588e-07 -9.551 1Comparing z scores and PIPs
[1] 0.02089 genename region_tag susie_pip mu2 PVE z num_eqtl
7736 MST1R 3_35 2.778e-03 1066.54 8.816e-06 -12.646 3
38 RBM6 3_35 3.659e-04 898.10 9.778e-07 12.536 1
9298 KCTD13 16_24 3.260e-02 111.57 1.082e-05 11.491 1
5215 ADCY3 2_16 5.213e-05 181.06 2.808e-08 10.987 2
7732 RNF123 3_35 4.332e-12 814.77 1.050e-14 -10.959 1
1846 MAPK3 16_24 6.198e-03 99.06 1.827e-06 10.880 1
8639 INO80E 16_24 7.196e-03 95.02 2.034e-06 10.734 1
12763 RP11-1348G14.4 16_23 7.270e-02 92.18 1.994e-05 10.676 1
11175 NPIPB6 16_23 6.407e-02 94.15 1.795e-05 -10.506 1
10711 CLN3 16_23 3.079e-02 89.34 8.184e-06 10.453 1
9418 NUPR1 16_23 7.178e-02 98.60 2.106e-05 -10.437 2
9502 NFATC2IP 16_23 2.729e-02 87.47 7.102e-06 -10.013 1
8296 ZNF668 16_24 3.291e-02 78.13 7.649e-06 10.000 1
8995 C1QTNF4 11_29 7.823e-03 95.03 2.212e-06 9.961 2
12572 ETV5 3_114 6.941e-01 94.99 1.962e-04 9.862 1
1938 KAT8 16_24 6.258e-03 74.20 1.381e-06 -9.848 1
11718 NDUFS3 11_29 4.101e-03 85.99 1.049e-06 -9.624 1
11003 SULT1A2 16_23 8.563e-03 77.50 1.975e-06 -9.621 2
11724 LAT 16_23 5.360e-02 86.34 1.377e-05 -9.553 1
2577 MTCH2 11_29 3.824e-03 84.27 9.588e-07 -9.551 1GO enrichment analysis for genes with PIP>0.5
#number of genes for gene set enrichment
length(genes)[1] 7Uploading data to Enrichr... Done.
Querying GO_Biological_Process_2021... Done.
Querying GO_Cellular_Component_2021... Done.
Querying GO_Molecular_Function_2021... Done.
Parsing results... Done.
[1] "GO_Biological_Process_2021"
Term
1 tricuspid valve development (GO:0003175)
2 tricuspid valve morphogenesis (GO:0003186)
3 pulmonary artery morphogenesis (GO:0061156)
4 ventricular cardiac muscle cell differentiation (GO:0055012)
5 ventricular cardiac muscle cell development (GO:0055015)
6 negative regulation of cardiocyte differentiation (GO:1905208)
7 vascular associated smooth muscle cell development (GO:0097084)
8 dorsal aorta development (GO:0035907)
9 dorsal aorta morphogenesis (GO:0035912)
10 vascular associated smooth muscle cell differentiation (GO:0035886)
11 response to hydroperoxide (GO:0033194)
12 negative regulation of vascular associated smooth muscle cell differentiation (GO:1905064)
13 positive regulation of transcription by RNA polymerase II (GO:0045944)
14 epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)
15 negative regulation of biomineralization (GO:0110150)
16 DNA dealkylation (GO:0035510)
17 DNA dealkylation involved in DNA repair (GO:0006307)
18 atrial septum morphogenesis (GO:0060413)
19 Notch signaling involved in heart development (GO:0061314)
20 regulation of transcription, DNA-templated (GO:0006355)
21 smooth muscle cell differentiation (GO:0051145)
22 positive regulation of vascular endothelial cell proliferation (GO:1905564)
23 cardiac right ventricle morphogenesis (GO:0003215)
24 regulation of gene expression (GO:0010468)
25 cardiac left ventricle morphogenesis (GO:0003214)
26 atrial septum development (GO:0003283)
27 regulation of vasculogenesis (GO:2001212)
28 negative regulation of transcription regulatory region DNA binding (GO:2000678)
29 positive regulation by host of viral transcription (GO:0043923)
30 pulmonary valve morphogenesis (GO:0003184)
31 cell surface receptor signaling pathway involved in heart development (GO:0061311)
32 aorta morphogenesis (GO:0035909)
33 positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)
34 muscle tissue morphogenesis (GO:0060415)
35 positive regulation of transcription, DNA-templated (GO:0045893)
36 positive regulation of amyloid-beta formation (GO:1902004)
37 pulmonary valve development (GO:0003177)
38 regulation of vascular endothelial cell proliferation (GO:1905562)
39 cardiac atrium morphogenesis (GO:0003209)
40 atrioventricular valve morphogenesis (GO:0003181)
41 mesenchymal cell development (GO:0014031)
42 cardiac epithelial to mesenchymal transition (GO:0060317)
43 cardiac ventricle development (GO:0003231)
44 positive regulation of cyclin-dependent protein kinase activity (GO:1904031)
45 positive regulation of macromolecule metabolic process (GO:0010604)
46 positive regulation of amyloid precursor protein catabolic process (GO:1902993)
47 negative regulation of biomineral tissue development (GO:0070168)
48 cardiac muscle cell development (GO:0055013)
49 cardiac conduction system development (GO:0003161)
50 regulation of nucleic acid-templated transcription (GO:1903506)
51 positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)
52 maturation of LSU-rRNA (GO:0000470)
53 regulation of biomineral tissue development (GO:0070167)
54 regulation of transcription regulatory region DNA binding (GO:2000677)
55 ventricular septum morphogenesis (GO:0060412)
56 artery morphogenesis (GO:0048844)
57 regulation of cellular macromolecule biosynthetic process (GO:2000112)
58 negative regulation of DNA binding (GO:0043392)
59 modulation by host of symbiont process (GO:0051851)
60 aortic valve morphogenesis (GO:0003180)
61 positive regulation of gene expression (GO:0010628)
62 vasculogenesis (GO:0001570)
63 muscle cell development (GO:0055001)
64 regulation of amyloid-beta formation (GO:1902003)
65 positive regulation of cell cycle G1/S phase transition (GO:1902808)
66 muscle cell differentiation (GO:0042692)
67 aortic valve development (GO:0003176)
68 positive regulation of nucleic acid-templated transcription (GO:1903508)
69 ventricular septum development (GO:0003281)
70 regulation of cell development (GO:0060284)
71 regulation of nervous system development (GO:0051960)
72 cardiac ventricle morphogenesis (GO:0003208)
73 epithelial to mesenchymal transition (GO:0001837)
74 positive regulation of blood vessel endothelial cell migration (GO:0043536)
75 mesenchymal cell differentiation (GO:0048762)
76 heart morphogenesis (GO:0003007)
77 cardiac muscle tissue development (GO:0048738)
78 regulation of cyclin-dependent protein kinase activity (GO:1904029)
79 regulation of blood vessel endothelial cell migration (GO:0043535)
80 blood vessel morphogenesis (GO:0048514)
81 ribosomal large subunit biogenesis (GO:0042273)
82 positive regulation of mitotic cell cycle phase transition (GO:1901992)
83 Notch signaling pathway (GO:0007219)
84 regulation of neurogenesis (GO:0050767)
85 anterior/posterior pattern specification (GO:0009952)
86 negative regulation of transcription by RNA polymerase II (GO:0000122)
87 regulation of transcription initiation from RNA polymerase II promoter (GO:0060260)
88 positive regulation of cell cycle (GO:0045787)
89 embryonic organ development (GO:0048568)
90 snRNA transcription by RNA polymerase II (GO:0042795)
91 regulation of G1/S transition of mitotic cell cycle (GO:2000045)
92 snRNA transcription (GO:0009301)
93 negative regulation of developmental process (GO:0051093)
94 positive regulation of endothelial cell proliferation (GO:0001938)
95 positive regulation of cellular amide metabolic process (GO:0034250)
96 regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)
97 positive regulation of endothelial cell migration (GO:0010595)
98 mitochondrial translational elongation (GO:0070125)
99 mitochondrial translational termination (GO:0070126)
100 regulation of lipid metabolic process (GO:0019216)
101 translational termination (GO:0006415)
102 regulation of transcription by RNA polymerase II (GO:0006357)
103 cellular response to chemical stress (GO:0062197)
104 positive regulation of vasculature development (GO:1904018)
105 translational elongation (GO:0006414)
106 mitochondrial translation (GO:0032543)
107 positive regulation of protein serine/threonine kinase activity (GO:0071902)
108 regulation of protein serine/threonine kinase activity (GO:0071900)
Overlap Adjusted.P.value Genes
1 1/5 0.02173 HEY2
2 1/5 0.02173 HEY2
3 1/5 0.02173 HEY2
4 1/5 0.02173 HEY2
5 1/6 0.02173 HEY2
6 1/7 0.02173 HEY2
7 1/7 0.02173 HEY2
8 1/7 0.02173 HEY2
9 1/7 0.02173 HEY2
10 1/8 0.02173 HEY2
11 1/8 0.02173 SP1
12 1/8 0.02173 HEY2
13 3/908 0.02173 SP1;HEY2;ETV5
14 1/9 0.02173 HEY2
15 1/9 0.02173 HEY2
16 1/10 0.02173 ASCC2
17 1/10 0.02173 ASCC2
18 1/11 0.02173 HEY2
19 1/11 0.02173 HEY2
20 4/2244 0.02173 SP1;HEY2;ASCC2;ETV5
21 1/12 0.02173 HEY2
22 1/13 0.02173 SP1
23 1/13 0.02173 HEY2
24 3/1079 0.02173 SP1;HEY2;ASCC2
25 1/14 0.02173 HEY2
26 1/14 0.02173 HEY2
27 1/14 0.02173 HEY2
28 1/16 0.02173 HEY2
29 1/16 0.02173 SP1
30 1/17 0.02173 HEY2
31 1/17 0.02173 HEY2
32 1/17 0.02173 HEY2
33 1/17 0.02173 CCND2
34 1/17 0.02173 HEY2
35 3/1183 0.02173 SP1;HEY2;ETV5
36 1/18 0.02173 SP1
37 1/18 0.02173 HEY2
38 1/18 0.02173 SP1
39 1/19 0.02173 HEY2
40 1/19 0.02173 HEY2
41 1/19 0.02173 HEY2
42 1/20 0.02173 HEY2
43 1/20 0.02173 HEY2
44 1/20 0.02173 CCND2
45 2/384 0.02205 SP1;HEY2
46 1/22 0.02237 SP1
47 1/22 0.02237 HEY2
48 1/24 0.02343 HEY2
49 1/25 0.02343 HEY2
50 2/430 0.02343 SP1;ASCC2
51 1/26 0.02343 CCND2
52 1/26 0.02343 MRPL1
53 1/26 0.02343 HEY2
54 1/27 0.02388 HEY2
55 1/28 0.02431 HEY2
56 1/30 0.02500 HEY2
57 2/468 0.02500 SP1;ASCC2
58 1/31 0.02500 HEY2
59 1/32 0.02500 SP1
60 1/32 0.02500 HEY2
61 2/482 0.02500 SP1;HEY2
62 1/33 0.02500 HEY2
63 1/33 0.02500 HEY2
64 1/34 0.02530 SP1
65 1/35 0.02530 CCND2
66 1/35 0.02530 HEY2
67 1/36 0.02531 HEY2
68 2/511 0.02531 SP1;HEY2
69 1/38 0.02626 HEY2
70 1/41 0.02792 HEY2
71 1/42 0.02819 HEY2
72 1/44 0.02911 HEY2
73 1/47 0.03066 HEY2
74 1/48 0.03088 SP1
75 1/51 0.03236 HEY2
76 1/53 0.03275 HEY2
77 1/53 0.03275 HEY2
78 1/54 0.03293 CCND2
79 1/55 0.03311 SP1
80 1/56 0.03329 HEY2
81 1/57 0.03346 MRPL1
82 1/58 0.03363 CCND2
83 1/60 0.03436 HEY2
84 1/62 0.03485 HEY2
85 1/63 0.03485 HEY2
86 2/684 0.03485 HEY2;ETV5
87 1/64 0.03494 HEY2
88 1/66 0.03521 CCND2
89 1/66 0.03521 HEY2
90 1/70 0.03662 SP1
91 1/71 0.03662 CCND2
92 1/71 0.03662 SP1
93 1/77 0.03883 HEY2
94 1/77 0.03883 SP1
95 1/81 0.04040 SP1
96 1/82 0.04046 CCND2
97 1/86 0.04197 SP1
98 1/89 0.04254 MRPL1
99 1/89 0.04254 MRPL1
100 1/92 0.04352 SP1
101 1/96 0.04477 MRPL1
102 3/2206 0.04477 SP1;HEY2;ETV5
103 1/101 0.04632 ETV5
104 1/102 0.04632 SP1
105 1/104 0.04676 MRPL1
106 1/105 0.04676 MRPL1
107 1/106 0.04676 CCND2
108 1/111 0.04848 CCND2
[1] "GO_Cellular_Component_2021"
Term Overlap
1 nucleus (GO:0005634) 5/4484
2 cyclin-dependent protein kinase holoenzyme complex (GO:0000307) 1/30
3 serine/threonine protein kinase complex (GO:1902554) 1/37
4 intracellular membrane-bounded organelle (GO:0043231) 5/5192
5 cytosolic large ribosomal subunit (GO:0022625) 1/55
6 large ribosomal subunit (GO:0015934) 1/59
Adjusted.P.value Genes
1 0.04435 CCND2;SP1;HEY2;ASCC2;ETV5
2 0.04435 CCND2
3 0.04435 CCND2
4 0.04435 CCND2;SP1;HEY2;ASCC2;ETV5
5 0.04435 MRPL1
6 0.04435 MRPL1
[1] "GO_Molecular_Function_2021"
Term
1 histone deacetylase binding (GO:0042826)
2 double-stranded DNA binding (GO:0003690)
3 sequence-specific DNA binding (GO:0043565)
4 sequence-specific double-stranded DNA binding (GO:1990837)
5 RNA polymerase II-specific DNA-binding transcription factor binding (GO:0061629)
6 DNA binding (GO:0003677)
7 DNA-binding transcription factor binding (GO:0140297)
8 transcription regulatory region nucleic acid binding (GO:0001067)
9 DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)
10 bHLH transcription factor binding (GO:0043425)
11 RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977)
12 transcription cis-regulatory region binding (GO:0000976)
13 cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)
14 ubiquitin binding (GO:0043130)
15 protein kinase regulator activity (GO:0019887)
Overlap Adjusted.P.value Genes
1 2/93 0.006236 SP1;HEY2
2 3/651 0.006236 SP1;HEY2;ETV5
3 3/707 0.006236 SP1;HEY2;ETV5
4 3/712 0.006236 SP1;HEY2;ETV5
5 2/190 0.006236 SP1;HEY2
6 3/811 0.006236 SP1;HEY2;ETV5
7 2/208 0.006236 SP1;HEY2
8 2/212 0.006236 SP1;ETV5
9 2/333 0.013425 SP1;ETV5
10 1/22 0.016887 SP1
11 3/1359 0.017807 SP1;HEY2;ETV5
12 2/549 0.025894 SP1;ETV5
13 1/44 0.025894 CCND2
14 1/74 0.040257 ASCC2
15 1/98 0.049580 CCND2DisGeNET enrichment analysis for genes with PIP>0.5
Description FDR
11 Communicating Hydrocephalus 0.01406
31 POLYDACTYLY, POSTAXIAL 0.01406
35 Hydrocephalus Ex-Vacuo 0.01406
46 Post-Traumatic Hydrocephalus 0.01406
48 Obstructive Hydrocephalus 0.01406
60 Cerebral ventriculomegaly 0.01406
63 Brugada ECG Pattern 0.01406
64 Perisylvian syndrome 0.01406
66 Megalanecephaly Polymicrogyria-Polydactyly Hydrocephalus Syndrome 0.01406
67 POSTAXIAL POLYDACTYLY, TYPE B 0.01406
Ratio BgRatio
11 1/4 7/9703
31 1/4 4/9703
35 1/4 7/9703
46 1/4 7/9703
48 1/4 7/9703
60 1/4 7/9703
63 1/4 4/9703
64 1/4 4/9703
66 1/4 4/9703
67 1/4 3/9703WebGestalt enrichment analysis for genes with PIP>0.5
Loading the functional categories...
Loading the ID list...
Loading the reference list...
Performing the enrichment analysis...
description size overlap FDR database
1 Transcriptional misregulation in cancer 83 3 0.04417 pathway_KEGG
userId
1 SP1;ETV5;CCND2PIP Manhattan Plot
Sensitivity, specificity and precision for silver standard genes
#number of genes in known annotations
print(length(known_annotations))[1] 41#number of genes in known annotations with imputed expression
print(sum(known_annotations %in% ctwas_gene_res$genename))[1] 24#significance threshold for TWAS
print(sig_thresh)[1] 4.595#number of ctwas genes
length(ctwas_genes)[1] 4#number of TWAS genes
length(twas_genes)[1] 241#show novel genes (ctwas genes with not in TWAS genes)
ctwas_gene_res[ctwas_gene_res$genename %in% novel_genes,report_cols] genename region_tag susie_pip mu2 PVE z num_eqtl
8605 MRPL1 4_52 1.0000 16661 0.04957 3.486 1
1577 ASCC2 22_10 0.9937 9364 0.02769 -2.618 1#sensitivity / recall
print(sensitivity) ctwas TWAS
0.00000 0.09756 #specificity
print(specificity) ctwas TWAS
0.9997 0.9794 #precision / PPV
print(precision) ctwas TWAS
0.0000 0.0166 
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] readxl_1.3.1 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7
[5] purrr_0.3.4 readr_2.1.1 tidyr_1.1.4 tidyverse_1.3.1
[9] tibble_3.1.6 WebGestaltR_0.4.4 disgenet2r_0.99.2 enrichR_3.0
[13] cowplot_1.0.0 ggplot2_3.3.5 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] fs_1.5.2 lubridate_1.8.0 bit64_4.0.5 doParallel_1.0.16
[5] httr_1.4.2 rprojroot_2.0.2 tools_3.6.1 backports_1.4.1
[9] doRNG_1.8.2 utf8_1.2.2 R6_2.5.1 vipor_0.4.5
[13] DBI_1.1.1 colorspace_2.0-2 withr_2.4.3 ggrastr_1.0.1
[17] tidyselect_1.1.1 bit_4.0.4 curl_4.3.2 compiler_3.6.1
[21] git2r_0.26.1 cli_3.1.0 rvest_1.0.2 Cairo_1.5-12.2
[25] xml2_1.3.3 labeling_0.4.2 scales_1.1.1 apcluster_1.4.8
[29] digest_0.6.29 rmarkdown_2.11 svglite_1.2.2 pkgconfig_2.0.3
[33] htmltools_0.5.2 dbplyr_2.1.1 fastmap_1.1.0 highr_0.9
[37] rlang_0.4.12 rstudioapi_0.13 RSQLite_2.2.8 jquerylib_0.1.4
[41] farver_2.1.0 generics_0.1.1 jsonlite_1.7.2 vroom_1.5.7
[45] magrittr_2.0.1 Matrix_1.2-18 ggbeeswarm_0.6.0 Rcpp_1.0.7
[49] munsell_0.5.0 fansi_0.5.0 gdtools_0.1.9 lifecycle_1.0.1
[53] stringi_1.7.6 whisker_0.3-2 yaml_2.2.1 plyr_1.8.6
[57] grid_3.6.1 blob_1.2.2 ggrepel_0.9.1 parallel_3.6.1
[61] promises_1.0.1 crayon_1.4.2 lattice_0.20-38 haven_2.4.3
[65] hms_1.1.1 knitr_1.36 pillar_1.6.4 igraph_1.2.10
[69] rjson_0.2.20 rngtools_1.5.2 reshape2_1.4.4 codetools_0.2-16
[73] reprex_2.0.1 glue_1.5.1 evaluate_0.14 data.table_1.14.2
[77] modelr_0.1.8 vctrs_0.3.8 tzdb_0.2.0 httpuv_1.5.1
[81] foreach_1.5.1 cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1
[85] cachem_1.0.6 xfun_0.29 broom_0.7.10 later_0.8.0
[89] iterators_1.0.13 beeswarm_0.2.3 memoise_2.0.1 ellipsis_0.3.2