Last updated: 2023-02-23

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Knit directory: cTWAS_analysis/

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analysis_id <- params$analysis_id
trait_id <- params$trait_id
weight <- params$weight

results_dir <- paste0("/project2/xinhe/shengqian/cTWAS/cTWAS_analysis/data/", trait_id, "/", weight)

source("/project2/xinhe/shengqian/cTWAS/cTWAS_analysis/code/ctwas_config_b38.R")
options(digits = 4)

Load ctwas results

Check convergence of parameters

Version Author Date
26813a2 sq-96 2023-02-23
72d6af3 sq-96 2023-01-05
#estimated group prior
estimated_group_prior <- estimated_group_prior_all[,ncol(group_prior_rec)]
print(estimated_group_prior)
           SNP          Liver Liver_Splicing 
     0.0001129      0.0092207      0.0077965 
#estimated group prior variance
estimated_group_prior_var <- estimated_group_prior_var_all[,ncol(group_prior_var_rec)]
print(estimated_group_prior_var)
           SNP          Liver Liver_Splicing 
         12.94          38.08          19.66 
#estimated enrichment
estimated_enrichment <- estimated_enrichment_all[ncol(group_prior_var_rec)]
print(estimated_enrichment)
[1] 58.71
#report sample size
print(sample_size)
[1] 343621
#report group size
print(group_size)
           SNP          Liver Liver_Splicing 
       8696600          11003          21610 
#estimated group PVE
estimated_group_pve <- estimated_group_pve_all[,ncol(group_prior_rec)]
print(estimated_group_pve)
           SNP          Liver Liver_Splicing 
      0.036977       0.011243       0.009639 
#total PVE
sum(estimated_group_pve)
[1] 0.05786
#attributable PVE
estimated_group_pve/sum(estimated_group_pve)
           SNP          Liver Liver_Splicing 
        0.6391         0.1943         0.1666 

Top expression/intron/CpG units

      genename                      gene_id susie_pip      group region_tag
29766    PSRC1           ENSG00000134222.16    1.0000 Expression       1_67
32083     LDLR  intron_19_11120522_11123174    1.0000   Splicing       19_9
30995  ST3GAL4           ENSG00000110080.18    1.0000 Expression      11_77
31551      HPR            ENSG00000261701.6    1.0000 Expression      16_38
29938   INSIG2           ENSG00000125629.14    1.0000 Expression       2_69
29916    ABCG8            ENSG00000143921.6    0.9989 Expression       2_27
31573       HP  intron_16_72057466_72058254    0.9982   Splicing      16_38
30861    FADS1           ENSG00000149485.18    0.9977 Expression      11_34
30318   NPC1L1           ENSG00000015520.14    0.9948 Expression       7_32
30634    ABCA1           ENSG00000165029.15    0.9942 Expression       9_53
30610     TNKS           ENSG00000173273.15    0.9874 Expression       8_12
32542     PLTP           ENSG00000100979.14    0.9874 Expression      20_28
30284    HLA-C   intron_6_31270085_31355317    0.9870   Splicing       6_25
32234    PRKD2           ENSG00000105287.12    0.9863 Expression      19_33
31177     GAS6           ENSG00000183087.14    0.9849 Expression      13_62
32512    RRBP1           ENSG00000125844.15    0.9821 Expression      20_13
30485    LRCH4 intron_7_100575304_100575705    0.9795   Splicing       7_61
29981    INHBB            ENSG00000163083.5    0.9747 Expression       2_70
32157   CYP2A6            ENSG00000255974.7    0.9655 Expression      19_28
30093  CSNK1G3           ENSG00000151292.17    0.9614 Expression       5_75
31959     KDSR           ENSG00000119537.15    0.9570 Expression      18_35
30314      SP4           ENSG00000105866.13    0.9542 Expression       7_19
31706   STAT5B            ENSG00000173757.9    0.9493 Expression      17_25
30624   TTC39B           ENSG00000155158.20    0.9457 Expression       9_13
30795 C10orf88           ENSG00000119965.12    0.9401 Expression      10_77
30069     PELO           ENSG00000152684.10    0.9369 Expression       5_31
29984   ACVR1C           ENSG00000123612.15    0.9367 Expression       2_94
30173   TRIM39           ENSG00000204599.14    0.9250 Expression       6_25
30657     PKN3            ENSG00000160447.6    0.9216 Expression       9_66
30331    DDX56           ENSG00000136271.10    0.9191 Expression       7_32
29986    GSK3B           ENSG00000082701.14    0.9016 Expression       3_74
32255     FUT2           ENSG00000176920.11    0.8999 Expression      19_33
31522    ITGAL  intron_16_30505462_30506715    0.8965   Splicing      16_24
30623   KIF13B   intron_8_29092878_29099133    0.8776   Splicing       8_28
29813    CNIH4           ENSG00000143771.11    0.8710 Expression      1_114
29597  KLHDC7A            ENSG00000179023.8    0.8675 Expression       1_13
31082     PHC1    intron_12_8921750_8922633    0.8414   Splicing       12_9
29882     ALLC            ENSG00000151360.9    0.8407 Expression        2_2
30832  SPTY2D1           ENSG00000179119.14    0.8399 Expression      11_13
30552     POP7            ENSG00000172336.4    0.8373 Expression       7_62
31841    ABCA8  intron_17_68883882_68884331    0.8310   Splicing      17_39
29743     USP1           ENSG00000162607.12    0.8235 Expression       1_39
31415     LIPC  intron_15_58431776_58431993    0.8159   Splicing      15_26
32130  CYP4F12  intron_19_15685197_15696430    0.8051   Splicing      19_13

Top genes by expression/splicing/methylation pip

      genename susie_pip      group
12103       HP    1.0559   Splicing
13479    PARP9    1.0480   Splicing
12555    LRCH4    1.0307   Splicing
14673 SLC22A18    1.0244   Splicing
11442   ERGIC3    1.0111   Splicing
10054    ASGR1    1.0107   Splicing
9599     ABCA8    1.0070   Splicing
14498   SEC16B    1.0033   Splicing
12481     LDLR    1.0000   Splicing
6278     PSRC1    1.0000 Expression
7716   ST3GAL4    1.0000 Expression
3564       HPR    1.0000 Expression
3767    INSIG2    1.0000 Expression
43       ABCG8    0.9989 Expression
2672     FADS1    0.9977 Expression
5256    NPC1L1    0.9948 Expression
16       ABCA1    0.9942 Expression
10999  CYP4F12    0.9919   Splicing
12057    HLA-C    0.9876   Splicing
8364      TNKS    0.9874 Expression
5941      PLTP    0.9874 Expression
6176     PRKD2    0.9863 Expression
3056      GAS6    0.9849 Expression
6853     RRBP1    0.9821 Expression
13082    NADK2    0.9817   Splicing
14037      PXK    0.9804   Splicing
3753     INHBB    0.9747 Expression
9674      ACP6    0.9659   Splicing
1972    CYP2A6    0.9655 Expression
1875   CSNK1G3    0.9614 Expression
3962      KDSR    0.9570 Expression
7577       SP4    0.9542 Expression
7744    STAT5B    0.9493 Expression
8616    TTC39B    0.9457 Expression
896   C10orf88    0.9401 Expression
5695      PELO    0.9369 Expression
137     ACVR1C    0.9367 Expression
12291    ITGAL    0.9326   Splicing
8493    TRIM39    0.9250 Expression
5853      PKN3    0.9216 Expression
2105     DDX56    0.9191 Expression
12197   IL17RC    0.9039   Splicing
3333     GSK3B    0.9016 Expression
3002      FUT2    0.8999 Expression
12382   KIF13B    0.8776   Splicing
1664     CNIH4    0.8710 Expression
4035   KLHDC7A    0.8675 Expression
10473   CCDC57    0.8511   Splicing
12525     LIPC    0.8457   Splicing
13596     PHC1    0.8414   Splicing
334       ALLC    0.8407 Expression
7668   SPTY2D1    0.8399 Expression
6028      POP7    0.8373 Expression
11665    FLOT2    0.8269   Splicing
15748   UGT1A6    0.8245   Splicing
8803      USP1    0.8235 Expression
11660     FKRP    0.8103   Splicing
14938   SPRED2    0.8078   Splicing
13290    NR1I2    0.8014   Splicing

Top genes by combined PIP

      genename combined_pip expression_pip splicing_pip region_tag
2546     DDX56        1.455          0.919        0.536       7_32
2027     CNIH4        1.262          0.871        0.391      1_114
7614       PXK        1.217          0.237        0.980       3_40
9249   ST3GAL4        1.078          1.000        0.078      11_77
6681     PARP9        1.076          0.028        1.048       3_76
4312        HP        1.056          0.000        1.056      16_38
8419    SEC16B        1.038          0.035        1.003       1_87
6840      PELO        1.035          0.937        0.098       5_31
133       ACP6        1.033          0.067        0.966       1_73
5159     LRCH4        1.033          0.002        1.031       7_61
6332    NPC1L1        1.031          0.995        0.036       7_32
20       ABCA1        1.030          0.994        0.036       9_53
8702  SLC22A18        1.024          0.000        1.024       11_2
8204     RRBP1        1.016          0.982        0.034      20_13
760      ASGR1        1.011          0.000        1.011       17_6
3123    ERGIC3        1.011          0.000        1.011      20_21
10328   TTC39B        1.010          0.946        0.064       9_13
26       ABCA8        1.007          0.000        1.007      17_39
2421   CYP4F12        1.006          0.014        0.992      19_13
2397    CYP2A6        1.001          0.965        0.035      19_28
3708      GAS6        1.001          0.985        0.016      13_62
4319       HPR        1.000          1.000        0.000      16_38
4556    INSIG2        1.000          1.000        0.000       2_69
5028      LDLR        1.000          0.000        1.000       19_9
7410     PRKD2        1.000          0.986        0.014      19_33
7530     PSRC1        1.000          1.000        0.000       1_67
53       ABCG8        0.999          0.999        0.000       2_27
3247     FADS1        0.998          0.998        0.000      11_34
6032     NADK2        0.995          0.013        0.982       5_24
7128      PLTP        0.994          0.987        0.007      20_28
9879   TMEM199        0.990          0.548        0.442      17_17
4237     HLA-C        0.988          0.000        0.988       6_25
10029     TNKS        0.987          0.987        0.000       8_12
4539     INHBB        0.975          0.975        0.000       2_70
11450  ZSCAN31        0.974          0.421        0.553       6_22
2280   CSNK1G3        0.971          0.961        0.009       5_75
4787      KDSR        0.967          0.957        0.010      18_35
9084       SP4        0.954          0.954        0.000       7_19
9284    STAT5B        0.949          0.949        0.000      17_25
1128  C10orf88        0.940          0.940        0.000      10_77
171     ACVR1C        0.937          0.937        0.000       2_94
10605    USP53        0.936          0.152        0.785       4_77
4629     ITGAL        0.933          0.000        0.933      16_24
4483    IL17RC        0.925          0.021        0.904        3_8
10187   TRIM39        0.925          0.925        0.000       6_25
962      BCAT2        0.922          0.135        0.787      19_34
7027      PKN3        0.922          0.922        0.000       9_66
9218      SRRT        0.917          0.786        0.131       7_62
413       ALLC        0.914          0.841        0.073        2_2
4041     GSK3B        0.902          0.902        0.000       3_74
3641      FUT2        0.900          0.900        0.000      19_33
1079      BRI3        0.894          0.733        0.161       7_60
4816    KIF13B        0.878          0.000        0.878       8_28
6906      PHC1        0.873          0.031        0.841       12_9
4867   KLHDC7A        0.868          0.868        0.000       1_13
1480    CCDC57        0.867          0.016        0.851      17_47
9700     THOP1        0.862          0.123        0.739       19_3
5102      LIPC        0.858          0.012        0.846      15_26
6977    PIH1D1        0.853          0.111        0.742      19_34
9184   SPTY2D1        0.840          0.840        0.000      11_13
7236      POP7        0.837          0.837        0.000       7_62
10502   UGT1A6        0.835          0.010        0.825      2_137
2323      CTSH        0.832          0.639        0.193      15_37
3547     FLOT2        0.827          0.000        0.827      17_17
10569     USP1        0.823          0.823        0.000       1_39
9162    SPRED2        0.815          0.007        0.808       2_42
3537      FKRP        0.813          0.002        0.810      19_33
6365     NR1I2        0.813          0.011        0.801       3_74
7347    PPP6R2        0.813          0.022        0.791      22_24
9452     SYTL1        0.805          0.789        0.016       1_19

GO enrichment analysis for genes with PIP>0.5

#number of genes for gene set enrichment
length(genes)
[1] 70
Uploading 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"

Version Author Date
26813a2 sq-96 2023-02-23
                                                                          Term
1                                           cholesterol transport (GO:0030301)
2                                                sterol transport (GO:0015918)
3                                                 lipid transport (GO:0006869)
4                               intestinal cholesterol absorption (GO:0030299)
5                                         cholesterol homeostasis (GO:0042632)
6                                              sterol homeostasis (GO:0055092)
7                                     intestinal lipid absorption (GO:0098856)
8                                 peptidyl-serine phosphorylation (GO:0018105)
9                                    peptidyl-serine modification (GO:0018209)
10                                           xenobiotic transport (GO:0042908)
11                                             cholesterol efflux (GO:0033344)
12                                    organic substance transport (GO:0071702)
13                               regulation of cholesterol efflux (GO:0010874)
14                                  chylomicron remnant clearance (GO:0034382)
15                                        protein phosphorylation (GO:0006468)
16                          cellular response to sterol depletion (GO:0071501)
17                                             zymogen activation (GO:0031638)
18                                  protein poly-ADP-ribosylation (GO:0070212)
19                     negative regulation of cholesterol storage (GO:0010887)
20               negative regulation of protein metabolic process (GO:0051248)
21                          cellular protein modification process (GO:0006464)
22 cellular response to low-density lipoprotein particle stimulus (GO:0071404)
23                            membrane lipid biosynthetic process (GO:0046467)
24                                         phospholipid transport (GO:0015914)
25                             peptidyl-threonine phosphorylation (GO:0018107)
26                            intracellular cholesterol transport (GO:0032367)
27             positive regulation of protein export from nucleus (GO:0046827)
28                                  regulation of gene expression (GO:0010468)
29                              regulation of cholesterol storage (GO:0010885)
30                                  reverse cholesterol transport (GO:0043691)
31                                  receptor-mediated endocytosis (GO:0006898)
32                              positive regulation of cell death (GO:0010942)
33                                peptidyl-threonine modification (GO:0018210)
34                   high-density lipoprotein particle remodeling (GO:0034375)
35                             activin receptor signaling pathway (GO:0032924)
36                                       epoxygenase P450 pathway (GO:0019373)
   Overlap Adjusted.P.value
1     6/51        2.086e-05
2     4/21        3.495e-04
3    6/109        6.668e-04
4      3/9        7.542e-04
5     5/71        7.841e-04
6     5/72        7.841e-04
7     3/11        8.423e-04
8    6/156        1.972e-03
9    6/169        2.755e-03
10    3/20        3.983e-03
11    3/24        6.364e-03
12   5/136        8.484e-03
13    3/33        1.419e-02
14     2/7        1.590e-02
15   8/496        1.963e-02
16     2/9        2.375e-02
17    3/45        2.494e-02
18    2/10        2.494e-02
19    2/10        2.494e-02
20    3/52        3.453e-02
21 11/1025        3.453e-02
22    2/14        3.933e-02
23    3/58        3.933e-02
24    3/59        3.933e-02
25    3/60        3.933e-02
26    2/15        3.933e-02
27    2/15        3.933e-02
28 11/1079        3.933e-02
29    2/16        4.299e-02
30    2/17        4.453e-02
31   4/143        4.453e-02
32    3/66        4.453e-02
33    3/67        4.509e-02
34    2/18        4.654e-02
35    2/19        4.901e-02
36    2/19        4.901e-02
                                                                Genes
1                                  ABCA1;ABCG8;LIPC;NPC1L1;ABCA8;LDLR
2                                             ABCG8;NPC1L1;ABCA8;LDLR
3                                  ABCA1;ABCG8;NPC1L1;ABCA8;LDLR;PLTP
4                                                   ABCG8;NPC1L1;LDLR
5                                        ABCA1;ABCG8;LIPC;LDLR;TTC39B
6                                        ABCA1;ABCG8;LIPC;LDLR;TTC39B
7                                                   ABCG8;NPC1L1;LDLR
8                                  GSK3B;CSNK1G3;TNKS;PKN3;PRKD2;GAS6
9                                  GSK3B;CSNK1G3;TNKS;PKN3;PRKD2;GAS6
10                                               SLC22A18;NR1I2;ABCA8
11                                                  ABCA1;ABCG8;ABCA8
12                                    ABCA1;ABCG8;SLC22A18;ABCA8;PLTP
13                                                  ABCA8;PLTP;TTC39B
14                                                          LIPC;LDLR
15                      GSK3B;CSNK1G3;PXK;ACVR1C;TNKS;PKN3;PRKD2;GAS6
16                                                      INSIG2;NPC1L1
17                                                        HP;CTSH;HPR
18                                                         TNKS;PARP9
19                                                       ABCA1;TTC39B
20                                                   FLOT2;INHBB;LDLR
21   GSK3B;CSNK1G3;PXK;ACVR1C;TNKS;PKN3;ST3GAL4;PRKD2;PARP9;GAS6;FUT2
22                                                         ABCA1;LDLR
23                                                 ST3GAL4;PRKD2;KDSR
24                                                    ABCA1;LDLR;PLTP
25                                                   GSK3B;TNKS;PRKD2
26                                                         ABCA1;LDLR
27                                                         GSK3B;GAS6
28 GSK3B;SEC16B;TRIM39;SRRT;NR1I2;CTSH;FLOT2;PARP9;GAS6;SPTY2D1;FADS1
29                                                       ABCA1;TTC39B
30                                                         ABCA1;LIPC
31                                                  HP;HPR;LDLR;ASGR1
32                                                       GSK3B;HP;HPR
33                                                   GSK3B;TNKS;PRKD2
34                                                          LIPC;PLTP
35                                                       ACVR1C;INHBB
36                                                     CYP2A6;CYP4F12
[1] "GO_Cellular_Component_2021"

Version Author Date
26813a2 sq-96 2023-02-23
                                                     Term Overlap
1 COPII-coated ER to Golgi transport vesicle (GO:0030134)    4/79
  Adjusted.P.value                     Genes
1          0.02069 SEC16B;HLA-C;ERGIC3;CNIH4
[1] "GO_Molecular_Function_2021"

Version Author Date
26813a2 sq-96 2023-02-23
                                                   Term Overlap
1 low-density lipoprotein particle binding (GO:0030169)    3/17
2            cholesterol transfer activity (GO:0120020)    3/18
3                 sterol transfer activity (GO:0120015)    3/19
4             lipoprotein particle binding (GO:0071813)    3/24
5    arachidonic acid epoxygenase activity (GO:0008392)    2/16
6 phosphatidylcholine transporter activity (GO:0008525)    2/18
7  arachidonic acid monooxygenase activity (GO:0008391)    2/19
  Adjusted.P.value            Genes
1         0.001860   LIPC;LDLR;PLTP
2         0.001860 ABCA1;ABCG8;PLTP
3         0.001860 ABCA1;ABCG8;PLTP
4         0.002877   LIPC;LDLR;PLTP
5         0.040991   CYP2A6;CYP4F12
6         0.041441       ABCA1;PLTP
7         0.041441   CYP2A6;CYP4F12

DisGeNET enrichment analysis for genes with PIP>0.5

                       Description       FDR Ratio BgRatio
68  Hypercholesterolemia, Familial 0.0002243  4/39 18/9703
67            Hypercholesterolemia 0.0019056  4/39 39/9703
279  Hyperlipoproteinemia Type IIb 0.0019056  3/39 13/9703
241  Hyperlipoproteinemia Type IIa 0.0027752  3/39 16/9703
175                  Dyslipidemias 0.0065396  3/39 24/9703
234            Dyslipoproteinemias 0.0065396  3/39 24/9703
228           Hepatitis B, Chronic 0.0212185  2/39  8/9703
12                 Atherosclerosis 0.0286410  3/39 59/9703
18        Blood Platelet Disorders 0.0286410  2/39 16/9703
52                  Food Poisoning 0.0286410  1/39  1/9703

WebGestalt 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
1                                        Coronary Artery Disease  194      13
2                                                  Dyslipidaemia  111      10
3                                               Coronary Disease  222      12
4                                               Arteriosclerosis  217      11
5                                            Myocardial Ischemia  228      11
6                                           Hypercholesterolemia   78       7
7                                    Arterial Occlusive Diseases  216      10
8                                                 Heart Diseases  282      11
9                                         Cholesterol metabolism   44       5
10                                                       Obesity  228       9
11                                               Hyperlipidemias   88       6
12                                 familial hypercholesterolemia   55       5
13                                 Hyperlipoproteinemia Type III   10       3
14                                         Hyperlipoproteinemias   29       4
15                                  Hyperlipoproteinemia Type II   31       4
16                                       Cardiovascular Diseases  343      10
17                                             Vascular Diseases  285       9
18 Myopathy secondary to deficiency of selenium and/or vitamin E   41       4
         FDR       database
1  9.768e-07 disease_GLAD4U
2  3.550e-06 disease_GLAD4U
3  1.888e-05 disease_GLAD4U
4  1.117e-04 disease_GLAD4U
5  1.471e-04 disease_GLAD4U
6  3.352e-04 disease_GLAD4U
7  5.580e-04 disease_GLAD4U
8  7.526e-04 disease_GLAD4U
9  2.825e-03   pathway_KEGG
10 4.908e-03 disease_GLAD4U
11 5.749e-03 disease_GLAD4U
12 6.188e-03 disease_GLAD4U
13 6.188e-03 disease_GLAD4U
14 6.719e-03 disease_GLAD4U
15 8.223e-03 disease_GLAD4U
16 1.375e-02 disease_GLAD4U
17 1.640e-02 disease_GLAD4U
18 2.096e-02 disease_GLAD4U
                                                                        userId
1  HP;NPC1L1;ABCA1;TTC39B;INSIG2;LDLR;PSRC1;ABCG8;FADS1;PLTP;FUT2;LIPC;SPTY2D1
2                  NPC1L1;ABCA1;TTC39B;INSIG2;LDLR;PSRC1;ABCG8;FADS1;PLTP;LIPC
3          HP;NPC1L1;ABCA1;TTC39B;INSIG2;LDLR;PSRC1;ABCG8;FADS1;PLTP;FUT2;LIPC
4                  HP;NPC1L1;ABCA1;TTC39B;HPR;LDLR;PSRC1;ABCG8;FADS1;PLTP;LIPC
5               HP;NPC1L1;ABCA1;TTC39B;INSIG2;LDLR;PSRC1;ABCG8;FADS1;PLTP;LIPC
6                                     NPC1L1;ABCA1;INSIG2;LDLR;ABCG8;PLTP;LIPC
7                      HP;NPC1L1;ABCA1;TTC39B;LDLR;PSRC1;ABCG8;FADS1;PLTP;LIPC
8                 HP;NPC1L1;ABCA1;TTC39B;LDLR;PSRC1;ABCG8;FADS1;PLTP;LIPC;FKRP
9                                                   ABCA1;LDLR;ABCG8;PLTP;LIPC
10                          HP;SEC16B;ABCA1;TTC39B;INSIG2;LDLR;FADS1;PLTP;LIPC
11                                           NPC1L1;ABCA1;LDLR;ABCG8;PLTP;LIPC
12                                                NPC1L1;ABCA1;LDLR;ABCG8;LIPC
13                                                             ABCA1;LDLR;LIPC
14                                                      NPC1L1;ABCA1;LDLR;LIPC
15                                                      NPC1L1;ABCA1;LDLR;LIPC
16                       HP;ABCA1;TTC39B;GAS6;LDLR;PSRC1;ABCG8;FADS1;PLTP;LIPC
17                             HP;NPC1L1;ABCA1;GAS6;LDLR;PSRC1;ABCG8;PLTP;LIPC
18                                                        HP;NPC1L1;NADK2;PLTP
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':

    expand.grid, I, unname
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
#pdf(file = "./LDL_TEME199_locus.pdf", width = 5, height = 3.5)
#a <- locus_plot(region_tag="17_17", return_table=T,
#                      focus=NULL,
#                      label_genes=NULL,
#                      rerun_ctwas=F,
#                      rerun_load_only=F,
#                      label_panel="both",
#                      legend_side="left",
#                      legend_panel="cTWAS")
#dev.off()
ensembl <- useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")
locus_plot_gene_track_pub <- function(a, label_pos=NULL){
  chr <- unique(a$chrom)
  start <- min(a$pos)*1000000
  end <- max(a$pos)*1000000
  
  biomTrack <- BiomartGeneRegionTrack(chromosome = chr,
                                      start = start,
                                      end = end,
                                      name = "ENSEMBL",
                                      biomart = ensembl,
                                      filters=list(biotype="protein_coding"))
  
  
  biomTrack <- as(biomTrack, "GeneRegionTrack")
  biomTrack <- biomTrack[biomTrack@range@elementMetadata@listData$feature %in% c("protein_coding", "utr3", "utr5")]
  
  if (isTRUE(label_pos=="above")){
    displayPars(biomTrack)$just.group <- "above"
  }
  
  grid.newpage()
  
  plotTracks(biomTrack, collapseTranscripts = "meta", transcriptAnnotation = "symbol", from=start, to=end, panel.only=T, add=F)
}
#pdf(file = "./LDL_TEME199_genetrack.pdf", width = 3.86, height = 0.4)
#locus_plot_gene_track_pub(a, label_pos="above")
#dev.off()

sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.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] grid      stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] biomaRt_2.50.3       Gviz_1.38.4          GenomicRanges_1.46.1
 [4] GenomeInfoDb_1.30.1  IRanges_2.28.0       S4Vectors_0.32.4    
 [7] BiocGenerics_0.40.0  WebGestaltR_0.4.4    disgenet2r_0.99.2   
[10] enrichR_3.1          cowplot_1.1.1        ggplot2_3.4.0       
[13] workflowr_1.7.0     

loaded via a namespace (and not attached):
  [1] backports_1.2.1             Hmisc_4.7-2                
  [3] BiocFileCache_2.2.1         systemfonts_1.0.4          
  [5] plyr_1.8.8                  igraph_1.3.5               
  [7] lazyeval_0.2.2              splines_4.1.0              
  [9] BiocParallel_1.28.3         digest_0.6.31              
 [11] ensembldb_2.18.4            foreach_1.5.2              
 [13] htmltools_0.5.4             fansi_1.0.3                
 [15] checkmate_2.1.0             magrittr_2.0.3             
 [17] memoise_2.0.1               BSgenome_1.62.0            
 [19] cluster_2.1.2               doParallel_1.0.17          
 [21] tzdb_0.3.0                  Biostrings_2.62.0          
 [23] readr_2.1.3                 matrixStats_0.63.0         
 [25] vroom_1.6.0                 svglite_2.1.0              
 [27] prettyunits_1.1.1           jpeg_0.1-10                
 [29] colorspace_2.0-3            blob_1.2.3                 
 [31] rappdirs_0.3.3              xfun_0.35                  
 [33] dplyr_1.0.10                callr_3.7.3                
 [35] crayon_1.5.2                RCurl_1.98-1.9             
 [37] jsonlite_1.8.4              VariantAnnotation_1.40.0   
 [39] survival_3.2-11             iterators_1.0.14           
 [41] glue_1.6.2                  gtable_0.3.1               
 [43] zlibbioc_1.40.0             XVector_0.34.0             
 [45] DelayedArray_0.20.0         apcluster_1.4.10           
 [47] scales_1.2.1                DBI_1.1.3                  
 [49] rngtools_1.5.2              Rcpp_1.0.9                 
 [51] htmlTable_2.4.1             progress_1.2.2             
 [53] foreign_0.8-81              bit_4.0.5                  
 [55] Formula_1.2-4               htmlwidgets_1.6.0          
 [57] httr_1.4.4                  RColorBrewer_1.1-3         
 [59] ellipsis_0.3.2              pkgconfig_2.0.3            
 [61] XML_3.99-0.13               farver_2.1.0               
 [63] nnet_7.3-16                 sass_0.4.4                 
 [65] dbplyr_2.2.1                deldir_1.0-6               
 [67] utf8_1.2.2                  tidyselect_1.2.0           
 [69] labeling_0.4.2              rlang_1.0.6                
 [71] reshape2_1.4.4              later_1.3.0                
 [73] AnnotationDbi_1.56.2        munsell_0.5.0              
 [75] tools_4.1.0                 cachem_1.0.6               
 [77] cli_3.4.1                   generics_0.1.3             
 [79] RSQLite_2.2.19              evaluate_0.19              
 [81] stringr_1.5.0               fastmap_1.1.0              
 [83] yaml_2.3.6                  processx_3.8.0             
 [85] knitr_1.41                  bit64_4.0.5                
 [87] fs_1.5.2                    purrr_0.3.5                
 [89] AnnotationFilter_1.18.0     KEGGREST_1.34.0            
 [91] doRNG_1.8.2                 whisker_0.4.1              
 [93] xml2_1.3.3                  compiler_4.1.0             
 [95] rstudioapi_0.14             filelock_1.0.2             
 [97] curl_4.3.2                  png_0.1-8                  
 [99] tibble_3.1.8                bslib_0.4.1                
[101] stringi_1.7.8               highr_0.9                  
[103] ps_1.7.2                    GenomicFeatures_1.46.5     
[105] lattice_0.20-44             ProtGenerics_1.26.0        
[107] Matrix_1.3-3                vctrs_0.5.1                
[109] pillar_1.8.1                lifecycle_1.0.3            
[111] jquerylib_0.1.4             data.table_1.14.6          
[113] bitops_1.0-7                httpuv_1.6.7               
[115] rtracklayer_1.54.0          R6_2.5.1                   
[117] BiocIO_1.4.0                latticeExtra_0.6-30        
[119] promises_1.2.0.1            gridExtra_2.3              
[121] codetools_0.2-18            dichromat_2.0-0.1          
[123] assertthat_0.2.1            SummarizedExperiment_1.24.0
[125] rprojroot_2.0.3             rjson_0.2.21               
[127] withr_2.5.0                 GenomicAlignments_1.30.0   
[129] Rsamtools_2.10.0            GenomeInfoDbData_1.2.7     
[131] parallel_4.1.0              hms_1.1.2                  
[133] rpart_4.1-15                rmarkdown_2.19             
[135] MatrixGenerics_1.6.0        git2r_0.30.1               
[137] biovizBase_1.42.0           getPass_0.2-2              
[139] Biobase_2.54.0              base64enc_0.1-3            
[141] interp_1.1-3                restfulr_0.0.15