Investigating metabolites and proteins in relation to number of live births

library(TwoSampleMR)
## TwoSampleMR version 0.5.6 
## [>] New: Option to use non-European LD reference panels for clumping etc
## [>] Some studies temporarily quarantined to verify effect allele
## [>] See news(package='TwoSampleMR') and https://gwas.mrcieu.ac.uk for further details

Fatty acids

Ratio of docosahexaenoic acid to total fatty acids

d <- make_dat("met-d-DHA_pct", "ukb-b-1209")
## API: public: http://gwas-api.mrcieu.ac.uk/
## Extracting data for 28 SNP(s) from 1 GWAS(s)
## Finding proxies for 2 SNPs in outcome ukb-b-1209
## Extracting data for 2 SNP(s) from 1 GWAS(s)
## Harmonising Ratio of docosahexaenoic acid to total fatty acids || id:met-d-DHA_pct (met-d-DHA_pct) and Number of live births || id:ukb-b-1209 (ukb-b-1209)
d_mr<-mr(d)
## Analysing 'met-d-DHA_pct' on 'ukb-b-1209'
d_mr
##     id.exposure id.outcome                                outcome
## 1 met-d-DHA_pct ukb-b-1209 Number of live births || id:ukb-b-1209
## 2 met-d-DHA_pct ukb-b-1209 Number of live births || id:ukb-b-1209
## 3 met-d-DHA_pct ukb-b-1209 Number of live births || id:ukb-b-1209
## 4 met-d-DHA_pct ukb-b-1209 Number of live births || id:ukb-b-1209
## 5 met-d-DHA_pct ukb-b-1209 Number of live births || id:ukb-b-1209
##                                                                 exposure
## 1 Ratio of docosahexaenoic acid to total fatty acids || id:met-d-DHA_pct
## 2 Ratio of docosahexaenoic acid to total fatty acids || id:met-d-DHA_pct
## 3 Ratio of docosahexaenoic acid to total fatty acids || id:met-d-DHA_pct
## 4 Ratio of docosahexaenoic acid to total fatty acids || id:met-d-DHA_pct
## 5 Ratio of docosahexaenoic acid to total fatty acids || id:met-d-DHA_pct
##                      method nsnp          b         se         pval
## 1                  MR Egger   28 0.07719224 0.02482803 4.509007e-03
## 2           Weighted median   28 0.06168659 0.01238886 6.384885e-07
## 3 Inverse variance weighted   28 0.03729738 0.01898178 4.942535e-02
## 4               Simple mode   28 0.01837943 0.03900630 6.412892e-01
## 5             Weighted mode   28 0.06167064 0.01139656 1.010582e-05
mr_scatter_plot(d_mr,d)
## $`met-d-DHA_pct.ukb-b-1209`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##     id.exposure id.outcome
## 1 met-d-DHA_pct ukb-b-1209
d <- make_dat("ukb-b-1209", "met-d-DHA_pct")
## Extracting data for 11 SNP(s) from 1 GWAS(s)
## Harmonising Number of live births || id:ukb-b-1209 (ukb-b-1209) and Ratio of docosahexaenoic acid to total fatty acids || id:met-d-DHA_pct (met-d-DHA_pct)
d_mr<-mr(d)
## Analysing 'ukb-b-1209' on 'met-d-DHA_pct'
d_mr
##   id.exposure    id.outcome
## 1  ukb-b-1209 met-d-DHA_pct
## 2  ukb-b-1209 met-d-DHA_pct
## 3  ukb-b-1209 met-d-DHA_pct
## 4  ukb-b-1209 met-d-DHA_pct
## 5  ukb-b-1209 met-d-DHA_pct
##                                                                  outcome
## 1 Ratio of docosahexaenoic acid to total fatty acids || id:met-d-DHA_pct
## 2 Ratio of docosahexaenoic acid to total fatty acids || id:met-d-DHA_pct
## 3 Ratio of docosahexaenoic acid to total fatty acids || id:met-d-DHA_pct
## 4 Ratio of docosahexaenoic acid to total fatty acids || id:met-d-DHA_pct
## 5 Ratio of docosahexaenoic acid to total fatty acids || id:met-d-DHA_pct
##                                 exposure                    method nsnp
## 1 Number of live births || id:ukb-b-1209                  MR Egger   11
## 2 Number of live births || id:ukb-b-1209           Weighted median   11
## 3 Number of live births || id:ukb-b-1209 Inverse variance weighted   11
## 4 Number of live births || id:ukb-b-1209               Simple mode   11
## 5 Number of live births || id:ukb-b-1209             Weighted mode   11
##             b         se       pval
## 1 -7.84157927 9.42055880 0.42672371
## 2 -0.21368032 0.09526513 0.02489638
## 3  0.87106885 1.12634462 0.43930989
## 4 -0.04240575 0.15110503 0.78470877
## 5 -0.21994010 0.13127569 0.12479199
mr_scatter_plot(d_mr,d)
## $`ukb-b-1209.met-d-DHA_pct`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##   id.exposure    id.outcome
## 1  ukb-b-1209 met-d-DHA_pct

Seems to be some kind of relation between docosahexaenoic acid and number of children.

Ratio of omega-3 fatty acids to total fatty acids

d <- make_dat("met-d-Omega_3_pct", "ukb-b-1209")
## Extracting data for 41 SNP(s) from 1 GWAS(s)
## Finding proxies for 5 SNPs in outcome ukb-b-1209
## Extracting data for 5 SNP(s) from 1 GWAS(s)
## Harmonising Ratio of omega-3 fatty acids to total fatty acids || id:met-d-Omega_3_pct (met-d-Omega_3_pct) and Number of live births || id:ukb-b-1209 (ukb-b-1209)
d_mr<-mr(d)
## Analysing 'met-d-Omega_3_pct' on 'ukb-b-1209'
d_mr
##         id.exposure id.outcome                                outcome
## 1 met-d-Omega_3_pct ukb-b-1209 Number of live births || id:ukb-b-1209
## 2 met-d-Omega_3_pct ukb-b-1209 Number of live births || id:ukb-b-1209
## 3 met-d-Omega_3_pct ukb-b-1209 Number of live births || id:ukb-b-1209
## 4 met-d-Omega_3_pct ukb-b-1209 Number of live births || id:ukb-b-1209
## 5 met-d-Omega_3_pct ukb-b-1209 Number of live births || id:ukb-b-1209
##                                                                    exposure
## 1 Ratio of omega-3 fatty acids to total fatty acids || id:met-d-Omega_3_pct
## 2 Ratio of omega-3 fatty acids to total fatty acids || id:met-d-Omega_3_pct
## 3 Ratio of omega-3 fatty acids to total fatty acids || id:met-d-Omega_3_pct
## 4 Ratio of omega-3 fatty acids to total fatty acids || id:met-d-Omega_3_pct
## 5 Ratio of omega-3 fatty acids to total fatty acids || id:met-d-Omega_3_pct
##                      method nsnp           b          se         pval
## 1                  MR Egger   39 0.051211686 0.013175184 4.060594e-04
## 2           Weighted median   39 0.044948050 0.008823304 3.501387e-07
## 3 Inverse variance weighted   39 0.023497945 0.011734472 4.523404e-02
## 4               Simple mode   39 0.001903734 0.039169036 9.614902e-01
## 5             Weighted mode   39 0.044224673 0.008837348 1.309961e-05
mr_scatter_plot(d_mr,d)
## $`met-d-Omega_3_pct.ukb-b-1209`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##         id.exposure id.outcome
## 1 met-d-Omega_3_pct ukb-b-1209
d <- make_dat("ukb-b-1209", "met-d-Omega_3_pct")
## Extracting data for 11 SNP(s) from 1 GWAS(s)
## Harmonising Number of live births || id:ukb-b-1209 (ukb-b-1209) and Ratio of omega-3 fatty acids to total fatty acids || id:met-d-Omega_3_pct (met-d-Omega_3_pct)
d_mr<-mr(d)
## Analysing 'ukb-b-1209' on 'met-d-Omega_3_pct'
d_mr
##   id.exposure        id.outcome
## 1  ukb-b-1209 met-d-Omega_3_pct
## 2  ukb-b-1209 met-d-Omega_3_pct
## 3  ukb-b-1209 met-d-Omega_3_pct
## 4  ukb-b-1209 met-d-Omega_3_pct
## 5  ukb-b-1209 met-d-Omega_3_pct
##                                                                     outcome
## 1 Ratio of omega-3 fatty acids to total fatty acids || id:met-d-Omega_3_pct
## 2 Ratio of omega-3 fatty acids to total fatty acids || id:met-d-Omega_3_pct
## 3 Ratio of omega-3 fatty acids to total fatty acids || id:met-d-Omega_3_pct
## 4 Ratio of omega-3 fatty acids to total fatty acids || id:met-d-Omega_3_pct
## 5 Ratio of omega-3 fatty acids to total fatty acids || id:met-d-Omega_3_pct
##                                 exposure                    method nsnp
## 1 Number of live births || id:ukb-b-1209                  MR Egger   11
## 2 Number of live births || id:ukb-b-1209           Weighted median   11
## 3 Number of live births || id:ukb-b-1209 Inverse variance weighted   11
## 4 Number of live births || id:ukb-b-1209               Simple mode   11
## 5 Number of live births || id:ukb-b-1209             Weighted mode   11
##               b          se      pval
## 1 -10.955524497 13.25899774 0.4300098
## 2  -0.005262907  0.09592543 0.9562464
## 3   1.396782032  1.58617256 0.3785349
## 4   0.095041503  0.12813413 0.4753079
## 5   0.015863194  0.12523210 0.9017121
mr_scatter_plot(d_mr,d)
## $`ukb-b-1209.met-d-Omega_3_pct`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##   id.exposure        id.outcome
## 1  ukb-b-1209 met-d-Omega_3_pct

Ratio of omega-6 fatty acids to omega-3 fatty acids

d <- make_dat("met-d-Omega_6_by_Omega_3", "ukb-b-1209")
## Extracting data for 41 SNP(s) from 1 GWAS(s)
## Finding proxies for 6 SNPs in outcome ukb-b-1209
## Extracting data for 6 SNP(s) from 1 GWAS(s)
## Harmonising Ratio of omega-6 fatty acids to omega-3 fatty acids || id:met-d-Omega_6_by_Omega_3 (met-d-Omega_6_by_Omega_3) and Number of live births || id:ukb-b-1209 (ukb-b-1209)
d_mr<-mr(d)
## Analysing 'met-d-Omega_6_by_Omega_3' on 'ukb-b-1209'
d_mr
##                id.exposure id.outcome                                outcome
## 1 met-d-Omega_6_by_Omega_3 ukb-b-1209 Number of live births || id:ukb-b-1209
## 2 met-d-Omega_6_by_Omega_3 ukb-b-1209 Number of live births || id:ukb-b-1209
## 3 met-d-Omega_6_by_Omega_3 ukb-b-1209 Number of live births || id:ukb-b-1209
## 4 met-d-Omega_6_by_Omega_3 ukb-b-1209 Number of live births || id:ukb-b-1209
## 5 met-d-Omega_6_by_Omega_3 ukb-b-1209 Number of live births || id:ukb-b-1209
##                                                                             exposure
## 1 Ratio of omega-6 fatty acids to omega-3 fatty acids || id:met-d-Omega_6_by_Omega_3
## 2 Ratio of omega-6 fatty acids to omega-3 fatty acids || id:met-d-Omega_6_by_Omega_3
## 3 Ratio of omega-6 fatty acids to omega-3 fatty acids || id:met-d-Omega_6_by_Omega_3
## 4 Ratio of omega-6 fatty acids to omega-3 fatty acids || id:met-d-Omega_6_by_Omega_3
## 5 Ratio of omega-6 fatty acids to omega-3 fatty acids || id:met-d-Omega_6_by_Omega_3
##                      method nsnp           b          se         pval
## 1                  MR Egger   38 -0.05203355 0.014934244 1.315775e-03
## 2           Weighted median   38 -0.04923569 0.009294452 1.175144e-07
## 3 Inverse variance weighted   38 -0.02549387 0.012294867 3.812229e-02
## 4               Simple mode   38 -0.01265214 0.035120328 7.207077e-01
## 5             Weighted mode   38 -0.04394894 0.009233048 2.954197e-05
mr_scatter_plot(d_mr,d)
## $`met-d-Omega_6_by_Omega_3.ukb-b-1209`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##                id.exposure id.outcome
## 1 met-d-Omega_6_by_Omega_3 ukb-b-1209
d <- make_dat("ukb-b-1209", "met-d-Omega_6_by_Omega_3")
## Extracting data for 11 SNP(s) from 1 GWAS(s)
## Server code: 502; Server is possibly experiencing traffic, trying again...
## Retry succeeded!
## Harmonising Number of live births || id:ukb-b-1209 (ukb-b-1209) and Ratio of omega-6 fatty acids to omega-3 fatty acids || id:met-d-Omega_6_by_Omega_3 (met-d-Omega_6_by_Omega_3)
d_mr<-mr(d)
## Analysing 'ukb-b-1209' on 'met-d-Omega_6_by_Omega_3'
d_mr
##   id.exposure               id.outcome
## 1  ukb-b-1209 met-d-Omega_6_by_Omega_3
## 2  ukb-b-1209 met-d-Omega_6_by_Omega_3
## 3  ukb-b-1209 met-d-Omega_6_by_Omega_3
## 4  ukb-b-1209 met-d-Omega_6_by_Omega_3
## 5  ukb-b-1209 met-d-Omega_6_by_Omega_3
##                                                                              outcome
## 1 Ratio of omega-6 fatty acids to omega-3 fatty acids || id:met-d-Omega_6_by_Omega_3
## 2 Ratio of omega-6 fatty acids to omega-3 fatty acids || id:met-d-Omega_6_by_Omega_3
## 3 Ratio of omega-6 fatty acids to omega-3 fatty acids || id:met-d-Omega_6_by_Omega_3
## 4 Ratio of omega-6 fatty acids to omega-3 fatty acids || id:met-d-Omega_6_by_Omega_3
## 5 Ratio of omega-6 fatty acids to omega-3 fatty acids || id:met-d-Omega_6_by_Omega_3
##                                 exposure                    method nsnp
## 1 Number of live births || id:ukb-b-1209                  MR Egger   11
## 2 Number of live births || id:ukb-b-1209           Weighted median   11
## 3 Number of live births || id:ukb-b-1209 Inverse variance weighted   11
## 4 Number of live births || id:ukb-b-1209               Simple mode   11
## 5 Number of live births || id:ukb-b-1209             Weighted mode   11
##             b          se      pval
## 1 10.57578089 12.51263897 0.4198961
## 2 -0.02003834  0.09632017 0.8351986
## 3 -1.36372415  1.50020021 0.3633353
## 4 -0.21287935  0.12993180 0.1323789
## 5 -0.21287935  0.12506853 0.1195651
mr_scatter_plot(d_mr,d)
## $`ukb-b-1209.met-d-Omega_6_by_Omega_3`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##   id.exposure               id.outcome
## 1  ukb-b-1209 met-d-Omega_6_by_Omega_3

Ratio of linoleic acid to total fatty acids

d <- make_dat("met-d-LA_pct", "ukb-b-1209")
## Extracting data for 41 SNP(s) from 1 GWAS(s)
## Finding proxies for 8 SNPs in outcome ukb-b-1209
## Extracting data for 8 SNP(s) from 1 GWAS(s)
## Harmonising Ratio of linoleic acid to total fatty acids || id:met-d-LA_pct (met-d-LA_pct) and Number of live births || id:ukb-b-1209 (ukb-b-1209)
d_mr<-mr(d)
## Analysing 'met-d-LA_pct' on 'ukb-b-1209'
d_mr
##    id.exposure id.outcome                                outcome
## 1 met-d-LA_pct ukb-b-1209 Number of live births || id:ukb-b-1209
## 2 met-d-LA_pct ukb-b-1209 Number of live births || id:ukb-b-1209
## 3 met-d-LA_pct ukb-b-1209 Number of live births || id:ukb-b-1209
## 4 met-d-LA_pct ukb-b-1209 Number of live births || id:ukb-b-1209
## 5 met-d-LA_pct ukb-b-1209 Number of live births || id:ukb-b-1209
##                                                         exposure
## 1 Ratio of linoleic acid to total fatty acids || id:met-d-LA_pct
## 2 Ratio of linoleic acid to total fatty acids || id:met-d-LA_pct
## 3 Ratio of linoleic acid to total fatty acids || id:met-d-LA_pct
## 4 Ratio of linoleic acid to total fatty acids || id:met-d-LA_pct
## 5 Ratio of linoleic acid to total fatty acids || id:met-d-LA_pct
##                      method nsnp           b         se         pval
## 1                  MR Egger   38 -0.05850537 0.03651649 1.178591e-01
## 2           Weighted median   38 -0.08742717 0.01857947 2.531469e-06
## 3 Inverse variance weighted   38 -0.06452908 0.02251255 4.152217e-03
## 4               Simple mode   38 -0.02713910 0.04802657 5.754265e-01
## 5             Weighted mode   38 -0.08286234 0.01788929 4.370879e-05
mr_scatter_plot(d_mr,d)
## $`met-d-LA_pct.ukb-b-1209`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##    id.exposure id.outcome
## 1 met-d-LA_pct ukb-b-1209
d <- make_dat("ukb-b-1209", "met-d-LA_pct")
## Extracting data for 11 SNP(s) from 1 GWAS(s)
## Harmonising Number of live births || id:ukb-b-1209 (ukb-b-1209) and Ratio of linoleic acid to total fatty acids || id:met-d-LA_pct (met-d-LA_pct)
d_mr<-mr(d)
## Analysing 'ukb-b-1209' on 'met-d-LA_pct'
d_mr
##   id.exposure   id.outcome
## 1  ukb-b-1209 met-d-LA_pct
## 2  ukb-b-1209 met-d-LA_pct
## 3  ukb-b-1209 met-d-LA_pct
## 4  ukb-b-1209 met-d-LA_pct
## 5  ukb-b-1209 met-d-LA_pct
##                                                          outcome
## 1 Ratio of linoleic acid to total fatty acids || id:met-d-LA_pct
## 2 Ratio of linoleic acid to total fatty acids || id:met-d-LA_pct
## 3 Ratio of linoleic acid to total fatty acids || id:met-d-LA_pct
## 4 Ratio of linoleic acid to total fatty acids || id:met-d-LA_pct
## 5 Ratio of linoleic acid to total fatty acids || id:met-d-LA_pct
##                                 exposure                    method nsnp
## 1 Number of live births || id:ukb-b-1209                  MR Egger   11
## 2 Number of live births || id:ukb-b-1209           Weighted median   11
## 3 Number of live births || id:ukb-b-1209 Inverse variance weighted   11
## 4 Number of live births || id:ukb-b-1209               Simple mode   11
## 5 Number of live births || id:ukb-b-1209             Weighted mode   11
##            b         se      pval
## 1  6.2364217 6.03744638 0.3285818
## 2 -0.1436589 0.09527295 0.1315888
## 3 -0.8757577 0.74138263 0.2375037
## 4 -0.1616761 0.11545850 0.1916792
## 5 -0.1413941 0.10081509 0.1910369
mr_scatter_plot(d_mr,d)
## $`ukb-b-1209.met-d-LA_pct`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##   id.exposure   id.outcome
## 1  ukb-b-1209 met-d-LA_pct

Average number of double bonds in a fatty acid chain

d <- make_dat("met-c-851", "ukb-b-1209")
## Extracting data for 5 SNP(s) from 1 GWAS(s)
## Harmonising Average number of double bonds in a fatty acid chain || id:met-c-851 (met-c-851) and Number of live births || id:ukb-b-1209 (ukb-b-1209)
d_mr<-mr(d)
## Analysing 'met-c-851' on 'ukb-b-1209'
d_mr
##   id.exposure id.outcome                                outcome
## 1   met-c-851 ukb-b-1209 Number of live births || id:ukb-b-1209
## 2   met-c-851 ukb-b-1209 Number of live births || id:ukb-b-1209
## 3   met-c-851 ukb-b-1209 Number of live births || id:ukb-b-1209
## 4   met-c-851 ukb-b-1209 Number of live births || id:ukb-b-1209
## 5   met-c-851 ukb-b-1209 Number of live births || id:ukb-b-1209
##                                                               exposure
## 1 Average number of double bonds in a fatty acid chain || id:met-c-851
## 2 Average number of double bonds in a fatty acid chain || id:met-c-851
## 3 Average number of double bonds in a fatty acid chain || id:met-c-851
## 4 Average number of double bonds in a fatty acid chain || id:met-c-851
## 5 Average number of double bonds in a fatty acid chain || id:met-c-851
##                      method nsnp          b         se         pval
## 1                  MR Egger    5 0.11051936 0.02606174 0.0240107163
## 2           Weighted median    5 0.05459869 0.01276548 0.0000189381
## 3 Inverse variance weighted    5 0.04346156 0.02365157 0.0661249503
## 4               Simple mode    5 0.02641635 0.05884095 0.6767199636
## 5             Weighted mode    5 0.06053179 0.01206438 0.0073989318
mr_scatter_plot(d_mr,d)
## $`met-c-851.ukb-b-1209`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##   id.exposure id.outcome
## 1   met-c-851 ukb-b-1209
d <- make_dat("ukb-b-1209", "met-c-851")
## Extracting data for 11 SNP(s) from 1 GWAS(s)
## Finding proxies for 1 SNPs in outcome met-c-851
## Extracting data for 1 SNP(s) from 1 GWAS(s)
## Harmonising Number of live births || id:ukb-b-1209 (ukb-b-1209) and Average number of double bonds in a fatty acid chain || id:met-c-851 (met-c-851)
d_mr<-mr(d)
## Analysing 'ukb-b-1209' on 'met-c-851'
d_mr
##   id.exposure id.outcome
## 1  ukb-b-1209  met-c-851
## 2  ukb-b-1209  met-c-851
## 3  ukb-b-1209  met-c-851
## 4  ukb-b-1209  met-c-851
## 5  ukb-b-1209  met-c-851
##                                                                outcome
## 1 Average number of double bonds in a fatty acid chain || id:met-c-851
## 2 Average number of double bonds in a fatty acid chain || id:met-c-851
## 3 Average number of double bonds in a fatty acid chain || id:met-c-851
## 4 Average number of double bonds in a fatty acid chain || id:met-c-851
## 5 Average number of double bonds in a fatty acid chain || id:met-c-851
##                                 exposure                    method nsnp
## 1 Number of live births || id:ukb-b-1209                  MR Egger   11
## 2 Number of live births || id:ukb-b-1209           Weighted median   11
## 3 Number of live births || id:ukb-b-1209 Inverse variance weighted   11
## 4 Number of live births || id:ukb-b-1209               Simple mode   11
## 5 Number of live births || id:ukb-b-1209             Weighted mode   11
##             b        se      pval
## 1 -5.18886056 9.5671691 0.6007393
## 2  0.11263728 0.2434781 0.6436384
## 3  1.25346455 1.0903247 0.2502983
## 4  0.03894765 0.3295483 0.9082614
## 5  0.03894765 0.3038274 0.9005399
mr_scatter_plot(d_mr,d)
## $`ukb-b-1209.met-c-851`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##   id.exposure id.outcome
## 1  ukb-b-1209  met-c-851

Ratio of bisallylic groups to double bonds

d <- make_dat("met-c-844", "ukb-b-1209")
## Extracting data for 4 SNP(s) from 1 GWAS(s)
## Harmonising Ratio of bisallylic groups to double bonds || id:met-c-844 (met-c-844) and Number of live births || id:ukb-b-1209 (ukb-b-1209)
d_mr<-mr(d)
## Analysing 'met-c-844' on 'ukb-b-1209'
d_mr
##   id.exposure id.outcome                                outcome
## 1   met-c-844 ukb-b-1209 Number of live births || id:ukb-b-1209
## 2   met-c-844 ukb-b-1209 Number of live births || id:ukb-b-1209
## 3   met-c-844 ukb-b-1209 Number of live births || id:ukb-b-1209
## 4   met-c-844 ukb-b-1209 Number of live births || id:ukb-b-1209
## 5   met-c-844 ukb-b-1209 Number of live births || id:ukb-b-1209
##                                                     exposure
## 1 Ratio of bisallylic groups to double bonds || id:met-c-844
## 2 Ratio of bisallylic groups to double bonds || id:met-c-844
## 3 Ratio of bisallylic groups to double bonds || id:met-c-844
## 4 Ratio of bisallylic groups to double bonds || id:met-c-844
## 5 Ratio of bisallylic groups to double bonds || id:met-c-844
##                      method nsnp          b          se         pval
## 1                  MR Egger    4 0.07421357 0.016218957 4.459129e-02
## 2           Weighted median    4 0.03808019 0.008977588 2.218388e-05
## 3 Inverse variance weighted    4 0.03226724 0.015869075 4.201811e-02
## 4               Simple mode    4 0.01791620 0.028864158 5.787563e-01
## 5             Weighted mode    4 0.04077367 0.008788895 1.887440e-02
mr_scatter_plot(d_mr,d)
## $`met-c-844.ukb-b-1209`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##   id.exposure id.outcome
## 1   met-c-844 ukb-b-1209
d <- make_dat("ukb-b-1209", "met-c-844")
## Extracting data for 11 SNP(s) from 1 GWAS(s)
## Finding proxies for 1 SNPs in outcome met-c-844
## Extracting data for 1 SNP(s) from 1 GWAS(s)
## Harmonising Number of live births || id:ukb-b-1209 (ukb-b-1209) and Ratio of bisallylic groups to double bonds || id:met-c-844 (met-c-844)
d_mr<-mr(d)
## Analysing 'ukb-b-1209' on 'met-c-844'
d_mr
##   id.exposure id.outcome
## 1  ukb-b-1209  met-c-844
## 2  ukb-b-1209  met-c-844
## 3  ukb-b-1209  met-c-844
## 4  ukb-b-1209  met-c-844
## 5  ukb-b-1209  met-c-844
##                                                      outcome
## 1 Ratio of bisallylic groups to double bonds || id:met-c-844
## 2 Ratio of bisallylic groups to double bonds || id:met-c-844
## 3 Ratio of bisallylic groups to double bonds || id:met-c-844
## 4 Ratio of bisallylic groups to double bonds || id:met-c-844
## 5 Ratio of bisallylic groups to double bonds || id:met-c-844
##                                 exposure                    method nsnp
## 1 Number of live births || id:ukb-b-1209                  MR Egger   11
## 2 Number of live births || id:ukb-b-1209           Weighted median   11
## 3 Number of live births || id:ukb-b-1209 Inverse variance weighted   11
## 4 Number of live births || id:ukb-b-1209               Simple mode   11
## 5 Number of live births || id:ukb-b-1209             Weighted mode   11
##            b         se      pval
## 1 -8.7287916 14.5631679 0.5637051
## 2  0.1399114  0.2677501 0.6012911
## 3  1.8702132  1.6615533 0.2603428
## 4  0.1916314  0.3674524 0.6133627
## 5  0.1916314  0.3461964 0.5920580
mr_scatter_plot(d_mr,d)
## $`ukb-b-1209.met-c-844`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##   id.exposure id.outcome
## 1  ukb-b-1209  met-c-844

Tyrosine

d <- make_dat("met-d-Tyr", "ukb-b-1209")
## Extracting data for 38 SNP(s) from 1 GWAS(s)
## Finding proxies for 7 SNPs in outcome ukb-b-1209
## Extracting data for 7 SNP(s) from 1 GWAS(s)
## Harmonising Tyrosine || id:met-d-Tyr (met-d-Tyr) and Number of live births || id:ukb-b-1209 (ukb-b-1209)
d_mr<-mr(d)
## Analysing 'met-d-Tyr' on 'ukb-b-1209'
d_mr
##   id.exposure id.outcome                                outcome
## 1   met-d-Tyr ukb-b-1209 Number of live births || id:ukb-b-1209
## 2   met-d-Tyr ukb-b-1209 Number of live births || id:ukb-b-1209
## 3   met-d-Tyr ukb-b-1209 Number of live births || id:ukb-b-1209
## 4   met-d-Tyr ukb-b-1209 Number of live births || id:ukb-b-1209
## 5   met-d-Tyr ukb-b-1209 Number of live births || id:ukb-b-1209
##                   exposure                    method nsnp          b         se
## 1 Tyrosine || id:met-d-Tyr                  MR Egger   33 0.04864878 0.03352329
## 2 Tyrosine || id:met-d-Tyr           Weighted median   33 0.03499030 0.02081542
## 3 Tyrosine || id:met-d-Tyr Inverse variance weighted   33 0.02072539 0.02130489
## 4 Tyrosine || id:met-d-Tyr               Simple mode   33 0.04912795 0.04181901
## 5 Tyrosine || id:met-d-Tyr             Weighted mode   33 0.03287878 0.02038454
##         pval
## 1 0.15677113
## 2 0.09276681
## 3 0.33065301
## 4 0.24875262
## 5 0.11658033
mr_scatter_plot(d_mr,d)
## $`met-d-Tyr.ukb-b-1209`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##   id.exposure id.outcome
## 1   met-d-Tyr ukb-b-1209
d <- make_dat("ukb-b-1209", "met-d-Tyr")
## Extracting data for 11 SNP(s) from 1 GWAS(s)
## Harmonising Number of live births || id:ukb-b-1209 (ukb-b-1209) and Tyrosine || id:met-d-Tyr (met-d-Tyr)
d_mr<-mr(d)
## Analysing 'ukb-b-1209' on 'met-d-Tyr'
d_mr
##   id.exposure id.outcome                  outcome
## 1  ukb-b-1209  met-d-Tyr Tyrosine || id:met-d-Tyr
## 2  ukb-b-1209  met-d-Tyr Tyrosine || id:met-d-Tyr
## 3  ukb-b-1209  met-d-Tyr Tyrosine || id:met-d-Tyr
## 4  ukb-b-1209  met-d-Tyr Tyrosine || id:met-d-Tyr
## 5  ukb-b-1209  met-d-Tyr Tyrosine || id:met-d-Tyr
##                                 exposure                    method nsnp
## 1 Number of live births || id:ukb-b-1209                  MR Egger   11
## 2 Number of live births || id:ukb-b-1209           Weighted median   11
## 3 Number of live births || id:ukb-b-1209 Inverse variance weighted   11
## 4 Number of live births || id:ukb-b-1209               Simple mode   11
## 5 Number of live births || id:ukb-b-1209             Weighted mode   11
##            b         se      pval
## 1 -0.7449461 1.36947507 0.5996801
## 2 -0.1080754 0.09927805 0.2763246
## 3 -0.1931984 0.15781657 0.2208784
## 4 -0.1249099 0.16057294 0.4546381
## 5 -0.1118606 0.14737156 0.4653449
mr_scatter_plot(d_mr,d)
## $`ukb-b-1209.met-d-Tyr`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##   id.exposure id.outcome
## 1  ukb-b-1209  met-d-Tyr