BMI - Brain Amygdala

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Last updated: 2022-02-13

Checks: 6 1

Knit directory: cTWAS_analysis/

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absolute	relative
/project2/xinhe/shengqian/cTWAS/cTWAS_analysis/data/	data
/project2/xinhe/shengqian/cTWAS/cTWAS_analysis/code/ctwas_config.R	code/ctwas_config.R

Repository version: eb13ecf

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Ignored files:
    Ignored:    .ipynb_checkpoints/

Untracked files:
    Untracked:  code/.ipynb_checkpoints/
    Untracked:  code/AF_out/
    Untracked:  code/BMI_out/
    Untracked:  code/T2D_out/
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    Untracked:  code/run_BMI_analysis.sh
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    Untracked:  code/run_T2D_analysis.sh
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    Untracked:  data/UKBB/
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    Untracked:  data/gene_OMIM.txt
    Untracked:  data/gene_pip_0.8.txt
    Untracked:  data/mashr_Heart_Atrial_Appendage.db
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    Untracked:  data/untitled.txt

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/BMI_Brain_Amygdala.Rmd) and HTML (docs/BMI_Brain_Amygdala.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	eb13ecf	sq-96	2022-02-13	update
html	e6bc169	sq-96	2022-02-13	Build site.
Rmd	87fee8b	sq-96	2022-02-13	update

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Weight QC

[1] 10285

   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16 
1009  735  594  399  502  598  475  370  404  396  626  561  223  326  336  453 
  17   18   19   20   21   22 
 604  162  819  311  117  265 

[1] 8365

[1] 0.8133204

Load ctwas results

Check convergence of parameters

********************************************************

Note: As of version 1.0.0, cowplot does not change the

  default ggplot2 theme anymore. To recover the previous

  behavior, execute:
  theme_set(theme_cowplot())

********************************************************

Past versions of unnamed-chunk-4-1.png

Version	Author	Date
e6bc169	sq-96	2022-02-13

       gene         snp 
0.007851899 0.000294515 

    gene      snp 
22.60976 17.39546 

[1] 336107

[1]   10285 7535010

       gene         snp 
0.005432472 0.114854919 

[1]  0.185928 16.123047

Genes with highest PIPs

Past versions of unnamed-chunk-5-1.png

Version	Author	Date
e6bc169	sq-96	2022-02-13

          genename region_tag susie_pip         mu2          PVE         z
7067         PPM1M       3_36 0.9999997   203.84849 6.064986e-04  4.323157
9534          GSAP       7_49 0.9999978 31328.55559 9.320986e-02  5.259703
9062          TMIE       3_33 0.9988879    35.22577 1.046887e-04 -6.902292
3144         CCND2       12_4 0.9639272    29.09831 8.345155e-05 -5.119990
2362        B3GAT1      11_84 0.9273265    25.66174 7.080130e-05 -4.502212
7314         CASP7      10_71 0.8414194    24.92437 6.239635e-05  4.584307
1743          TSC2       16_2 0.8368816    30.80080 7.669172e-05  5.277516
10858      SLC12A8       3_77 0.8107856    22.51325 5.430835e-05 -4.338310
129         CELSR3       3_34 0.8057692    57.16502 1.370451e-04 -7.731481
4947          SUOX      12_35 0.7929490    57.58570 1.358571e-04 -5.806919
6745          TAL1       1_29 0.7916142    49.62828 1.168867e-04 -6.865849
7155         ZNF12        7_9 0.7763657    25.85263 5.971639e-05  4.971723
4469          HEY2       6_84 0.7704396 33571.88962 7.695500e-02  4.929525
12540 RP11-823E8.3      12_54 0.7460382    31.12767 6.909237e-05 -6.438012
8259        EFEMP2      11_36 0.7404485    97.56353 2.149338e-04 -7.541972
3049        PRRC2C       1_84 0.7401647    28.98860 6.383782e-05 -5.172951
2893        SLC1A4       2_42 0.7263618    23.45522 5.068914e-05 -4.046858
7589       NCKAP5L      12_31 0.7217699    48.19952 1.035056e-04 -8.217199
10874        VPS52       6_28 0.7097286   125.93060 2.659169e-04  1.606101
12020    LINC01977      17_45 0.7064264    28.56807 6.004409e-05  5.229978
      num_eqtl
7067         2
9534         1
9062         2
3144         1
2362         2
7314         1
1743         1
10858        1
129          1
4947         1
6745         1
7155         2
4469         1
12540        1
8259         2
3049         1
2893         1
7589         1
10874        1
12020        1

Genes with largest effect sizes

Past versions of unnamed-chunk-6-1.png

Version	Author	Date
e6bc169	sq-96	2022-02-13

      genename region_tag    susie_pip      mu2          PVE          z
9746   SLC38A3       3_35 0.000000e+00 67723.85 0.000000e+00   6.725828
7061     CAMKV       3_35 0.000000e+00 53039.36 0.000000e+00   9.847856
7212   CCDC171       9_13 0.000000e+00 50688.31 0.000000e+00   7.996551
7063     MST1R       3_35 0.000000e+00 34978.09 0.000000e+00 -12.601517
4469      HEY2       6_84 7.704396e-01 33571.89 7.695500e-02   4.929525
8838     DHFR2       3_59 0.000000e+00 32025.16 0.000000e+00   5.146136
9534      GSAP       7_49 9.999978e-01 31328.56 9.320986e-02   5.259703
8841     STX19       3_59 0.000000e+00 31018.31 0.000000e+00  -5.059656
7432      LEO1      15_21 2.077396e-07 27408.83 1.694073e-08   4.647326
5003    LYSMD2      15_21 0.000000e+00 26190.38 0.000000e+00  -4.402599
4997     MFAP1      15_16 1.607848e-07 23703.02 1.133891e-08   4.302998
7058    RNF123       3_35 0.000000e+00 23171.66 0.000000e+00 -10.957103
1259     WDR76      15_16 0.000000e+00 21159.20 0.000000e+00   4.858858
9777      DPYD       1_60 0.000000e+00 19617.83 0.000000e+00  -3.213351
849       MCM6       2_80 0.000000e+00 17859.24 0.000000e+00  -3.886179
4751   TUBGCP4      15_16 0.000000e+00 16922.11 0.000000e+00   3.371262
10116   ENTPD6      20_18 0.000000e+00 16404.93 0.000000e+00  -5.560735
8836     NSUN3       3_59 0.000000e+00 15636.11 0.000000e+00   4.755360
7782      ADAL      15_16 0.000000e+00 14787.91 0.000000e+00  -2.861302
7783     LCMT2      15_16 0.000000e+00 14375.85 0.000000e+00  -3.087238
      num_eqtl
9746         1
7061         1
7212         1
7063         2
4469         1
8838         1
9534         1
8841         1
7432         1
5003         1
4997         1
7058         1
1259         2
9777         1
849          1
4751         1
10116        1
8836         1
7782         1
7783         2

Genes with highest PVE

          genename region_tag  susie_pip         mu2          PVE         z
9534          GSAP       7_49 0.99999775 31328.55559 9.320986e-02  5.259703
4469          HEY2       6_84 0.77043964 33571.88962 7.695500e-02  4.929525
9966        TTC30B      2_107 0.31986906   757.36112 7.207716e-04 -3.137443
7067         PPM1M       3_36 0.99999975   203.84849 6.064986e-04  4.323157
10874        VPS52       6_28 0.70972860   125.93060 2.659169e-04  1.606101
8259        EFEMP2      11_36 0.74044851    97.56353 2.149338e-04 -7.541972
7134         SFXN1      5_105 0.07080249  1012.69819 2.133296e-04 -3.397633
129         CELSR3       3_34 0.80576915    57.16502 1.370451e-04 -7.731481
4947          SUOX      12_35 0.79294903    57.58570 1.358571e-04 -5.806919
6745          TAL1       1_29 0.79161423    49.62828 1.168867e-04 -6.865849
9062          TMIE       3_33 0.99888787    35.22577 1.046887e-04 -6.902292
7589       NCKAP5L      12_31 0.72176991    48.19952 1.035056e-04 -8.217199
9164         KCNB2       8_53 0.46637380    63.18433 8.767302e-05 -8.057392
3144         CCND2       12_4 0.96392719    29.09831 8.345155e-05 -5.119990
1743          TSC2       16_2 0.83688159    30.80080 7.669172e-05  5.277516
2362        B3GAT1      11_84 0.92732651    25.66174 7.080130e-05 -4.502212
12540 RP11-823E8.3      12_54 0.74603817    31.12767 6.909237e-05 -6.438012
8212         NEGR1       1_46 0.50118261    45.66722 6.809622e-05 -8.928461
3049        PRRC2C       1_84 0.74016474    28.98860 6.383782e-05 -5.172951
7314         CASP7      10_71 0.84141937    24.92437 6.239635e-05  4.584307
      num_eqtl
9534         1
4469         1
9966         1
7067         2
10874        1
8259         2
7134         1
129          1
4947         1
6745         1
9062         2
7589         1
9164         2
3144         1
1743         1
2362         2
12540        1
8212         1
3049         1
7314         1

Genes with largest z scores

            genename region_tag    susie_pip         mu2          PVE
7063           MST1R       3_35 0.000000e+00 34978.09479 0.000000e+00
7058          RNF123       3_35 0.000000e+00 23171.66318 0.000000e+00
5866           TAOK2      16_24 2.301334e-02    95.97347 6.571330e-06
11609 RP11-1348G14.4      16_23 1.472303e-01    90.56867 3.967325e-05
9939         SULT1A1      16_23 9.114419e-02    89.14576 2.417420e-05
10040        SULT1A2      16_23 9.114419e-02    89.14576 2.417420e-05
7566          ZNF668      16_24 1.131017e-01    77.72272 2.615409e-05
7567          ZNF646      16_24 1.131017e-01    77.72272 2.615409e-05
5192            SAE1      19_33 4.601078e-03   101.24760 1.386011e-06
7061           CAMKV       3_35 0.000000e+00 53039.36047 0.000000e+00
8211         C1QTNF4      11_29 3.022724e-02    96.81883 8.707246e-06
439            PRSS8      16_24 1.754656e-02    72.63603 3.791985e-06
7337           RAPSN      11_29 1.109988e-02    87.10822 2.876734e-06
10701            LAT      16_23 1.333217e-01    85.22211 3.380459e-05
2358           MTCH2      11_29 9.831627e-03    84.50940 2.472025e-06
11572    CTC-467M3.3       5_52 1.492286e-10   355.29867 1.577496e-13
8212           NEGR1       1_46 5.011826e-01    45.66722 6.809622e-05
7336           PSMC3      11_29 1.088521e-02    74.51731 2.413329e-06
1699           MAPK3      16_24 1.421618e-02    68.98855 2.917980e-06
12567          RCC1L       7_48 1.286620e-01    83.57640 3.199311e-05
               z num_eqtl
7063  -12.601517        2
7058  -10.957103        1
5866   10.737701        1
11609  10.603060        1
9939   10.415275        1
10040 -10.415275        1
7566   10.000364        1
7567  -10.000364        1
5192    9.848747        1
7061    9.847856        1
8211    9.834145        2
439    -9.764760        1
7337    9.613541        1
10701  -9.552834        1
2358   -9.514152        1
11572   9.482167        1
8212   -8.928461        1
7336   -8.866477        1
1699    8.826267        1
12567  -8.667336        1

Comparing z scores and PIPs

Past versions of unnamed-chunk-9-1.png

Version	Author	Date
e6bc169	sq-96	2022-02-13

Past versions of unnamed-chunk-9-2.png

Version	Author	Date
e6bc169	sq-96	2022-02-13

[1] 0.02129315

            genename region_tag    susie_pip         mu2          PVE
7063           MST1R       3_35 0.000000e+00 34978.09479 0.000000e+00
7058          RNF123       3_35 0.000000e+00 23171.66318 0.000000e+00
5866           TAOK2      16_24 2.301334e-02    95.97347 6.571330e-06
11609 RP11-1348G14.4      16_23 1.472303e-01    90.56867 3.967325e-05
9939         SULT1A1      16_23 9.114419e-02    89.14576 2.417420e-05
10040        SULT1A2      16_23 9.114419e-02    89.14576 2.417420e-05
7566          ZNF668      16_24 1.131017e-01    77.72272 2.615409e-05
7567          ZNF646      16_24 1.131017e-01    77.72272 2.615409e-05
5192            SAE1      19_33 4.601078e-03   101.24760 1.386011e-06
7061           CAMKV       3_35 0.000000e+00 53039.36047 0.000000e+00
8211         C1QTNF4      11_29 3.022724e-02    96.81883 8.707246e-06
439            PRSS8      16_24 1.754656e-02    72.63603 3.791985e-06
7337           RAPSN      11_29 1.109988e-02    87.10822 2.876734e-06
10701            LAT      16_23 1.333217e-01    85.22211 3.380459e-05
2358           MTCH2      11_29 9.831627e-03    84.50940 2.472025e-06
11572    CTC-467M3.3       5_52 1.492286e-10   355.29867 1.577496e-13
8212           NEGR1       1_46 5.011826e-01    45.66722 6.809622e-05
7336           PSMC3      11_29 1.088521e-02    74.51731 2.413329e-06
1699           MAPK3      16_24 1.421618e-02    68.98855 2.917980e-06
12567          RCC1L       7_48 1.286620e-01    83.57640 3.199311e-05
               z num_eqtl
7063  -12.601517        2
7058  -10.957103        1
5866   10.737701        1
11609  10.603060        1
9939   10.415275        1
10040 -10.415275        1
7566   10.000364        1
7567  -10.000364        1
5192    9.848747        1
7061    9.847856        1
8211    9.834145        2
439    -9.764760        1
7337    9.613541        1
10701  -9.552834        1
2358   -9.514152        1
11572   9.482167        1
8212   -8.928461        1
7336   -8.866477        1
1699    8.826267        1
12567  -8.667336        1

Sensitivity, specificity and precision for silver standard genes

[1] 41

[1] 22

[1] 4.57068

[1] 9

[1] 219

      genename region_tag susie_pip       mu2          PVE         z num_eqtl
7067     PPM1M       3_36 0.9999997 203.84849 6.064986e-04  4.323157        2
10858  SLC12A8       3_77 0.8107856  22.51325 5.430835e-05 -4.338310        1
2362    B3GAT1      11_84 0.9273265  25.66174 7.080130e-05 -4.502212        2

     ctwas       TWAS 
0.00000000 0.09756098 

    ctwas      TWAS 
0.9991231 0.9790510 

     ctwas       TWAS 
0.00000000 0.01826484 

Past versions of unnamed-chunk-10-1.png

Version	Author	Date
e6bc169	sq-96	2022-02-13

Session information

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    cowplot_1.0.0   ggplot2_3.3.5   workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.1  xfun_0.29         purrr_0.3.4       colorspace_2.0-2 
 [5] vctrs_0.3.8       generics_0.1.1    htmltools_0.5.2   yaml_2.2.1       
 [9] utf8_1.2.2        blob_1.2.2        rlang_0.4.12      jquerylib_0.1.4  
[13] later_0.8.0       pillar_1.6.4      glue_1.5.1        withr_2.4.3      
[17] DBI_1.1.1         bit64_4.0.5       lifecycle_1.0.1   stringr_1.4.0    
[21] cellranger_1.1.0  munsell_0.5.0     gtable_0.3.0      evaluate_0.14    
[25] memoise_2.0.1     labeling_0.4.2    knitr_1.36        fastmap_1.1.0    
[29] httpuv_1.5.1      fansi_0.5.0       highr_0.9         Rcpp_1.0.7       
[33] promises_1.0.1    scales_1.1.1      cachem_1.0.6      farver_2.1.0     
[37] fs_1.5.2          bit_4.0.4         digest_0.6.29     stringi_1.7.6    
[41] dplyr_1.0.7       rprojroot_2.0.2   grid_3.6.1        tools_3.6.1      
[45] magrittr_2.0.1    tibble_3.1.6      RSQLite_2.2.8     crayon_1.4.2     
[49] whisker_0.3-2     pkgconfig_2.0.3   ellipsis_0.3.2    data.table_1.14.2
[53] assertthat_0.2.1  rmarkdown_2.11    R6_2.5.1          git2r_0.26.1     
[57] compiler_3.6.1