Investigating various mental states in relation to number of children fathered

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

Feeling nervous

d <- make_dat("ebi-a-GCST006948", "ukb-b-2227")
## API: public: http://gwas-api.mrcieu.ac.uk/
## Extracting data for 35 SNP(s) from 1 GWAS(s)
## Harmonising Feeling nervous || id:ebi-a-GCST006948 (ebi-a-GCST006948) and Number of children fathered || id:ukb-b-2227 (ukb-b-2227)
d_mr<-mr(d)
## Analysing 'ebi-a-GCST006948' on 'ukb-b-2227'
d_mr
##        id.exposure id.outcome                                      outcome
## 1 ebi-a-GCST006948 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 2 ebi-a-GCST006948 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 3 ebi-a-GCST006948 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 4 ebi-a-GCST006948 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 5 ebi-a-GCST006948 ukb-b-2227 Number of children fathered || id:ukb-b-2227
##                                 exposure                    method nsnp
## 1 Feeling nervous || id:ebi-a-GCST006948                  MR Egger   35
## 2 Feeling nervous || id:ebi-a-GCST006948           Weighted median   35
## 3 Feeling nervous || id:ebi-a-GCST006948 Inverse variance weighted   35
## 4 Feeling nervous || id:ebi-a-GCST006948               Simple mode   35
## 5 Feeling nervous || id:ebi-a-GCST006948             Weighted mode   35
##             b         se        pval
## 1 -0.19934291 0.31593129 0.532406765
## 2 -0.07028820 0.04718799 0.136346316
## 3 -0.17596625 0.05608444 0.001703817
## 4 -0.07741519 0.09609722 0.426076323
## 5 -0.07741519 0.09081246 0.399916795
mr_scatter_plot(d_mr,d)
## $`ebi-a-GCST006948.ukb-b-2227`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##        id.exposure id.outcome
## 1 ebi-a-GCST006948 ukb-b-2227
d <- make_dat("ukb-b-2227", "ebi-a-GCST006948")
## Extracting data for 3 SNP(s) from 1 GWAS(s)
## Harmonising Number of children fathered || id:ukb-b-2227 (ukb-b-2227) and Feeling nervous || id:ebi-a-GCST006948 (ebi-a-GCST006948)
d_mr<-mr(d)
## Analysing 'ukb-b-2227' on 'ebi-a-GCST006948'
d_mr
##   id.exposure       id.outcome                                outcome
## 1  ukb-b-2227 ebi-a-GCST006948 Feeling nervous || id:ebi-a-GCST006948
## 2  ukb-b-2227 ebi-a-GCST006948 Feeling nervous || id:ebi-a-GCST006948
## 3  ukb-b-2227 ebi-a-GCST006948 Feeling nervous || id:ebi-a-GCST006948
## 4  ukb-b-2227 ebi-a-GCST006948 Feeling nervous || id:ebi-a-GCST006948
## 5  ukb-b-2227 ebi-a-GCST006948 Feeling nervous || id:ebi-a-GCST006948
##                                       exposure                    method nsnp
## 1 Number of children fathered || id:ukb-b-2227                  MR Egger    3
## 2 Number of children fathered || id:ukb-b-2227           Weighted median    3
## 3 Number of children fathered || id:ukb-b-2227 Inverse variance weighted    3
## 4 Number of children fathered || id:ukb-b-2227               Simple mode    3
## 5 Number of children fathered || id:ukb-b-2227             Weighted mode    3
##            b        se       pval
## 1 -2.3335661 8.2744424 0.82500485
## 2 -0.2527480 0.1480413 0.08776998
## 3 -0.4094079 0.3437494 0.23365079
## 4 -0.4522811 0.3205590 0.29371967
## 5 -0.0296460 0.1643903 0.87350529
mr_scatter_plot(d_mr,d)
## $`ukb-b-2227.ebi-a-GCST006948`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##   id.exposure       id.outcome
## 1  ukb-b-2227 ebi-a-GCST006948

Nervous feelings

d <- make_dat("ukb-b-20544", "ukb-b-2227")
## Extracting data for 58 SNP(s) from 1 GWAS(s)
## Harmonising Nervous feelings || id:ukb-b-20544 (ukb-b-20544) and Number of children fathered || id:ukb-b-2227 (ukb-b-2227)
## Removing the following SNPs for incompatible alleles:
## rs75892241
d_mr<-mr(d)
## Analysing 'ukb-b-20544' on 'ukb-b-2227'
d_mr
##   id.exposure id.outcome                                      outcome
## 1 ukb-b-20544 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 2 ukb-b-20544 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 3 ukb-b-20544 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 4 ukb-b-20544 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 5 ukb-b-20544 ukb-b-2227 Number of children fathered || id:ukb-b-2227
##                             exposure                    method nsnp           b
## 1 Nervous feelings || id:ukb-b-20544                  MR Egger   58 -0.70629331
## 2 Nervous feelings || id:ukb-b-20544           Weighted median   58 -0.16669495
## 3 Nervous feelings || id:ukb-b-20544 Inverse variance weighted   58 -0.39064316
## 4 Nervous feelings || id:ukb-b-20544               Simple mode   58 -0.01190211
## 5 Nervous feelings || id:ukb-b-20544             Weighted mode   58 -0.04021824
##           se         pval
## 1 0.49573796 0.1597843598
## 2 0.09208208 0.0702513629
## 3 0.09567226 0.0000444314
## 4 0.20672393 0.9542886188
## 5 0.20273253 0.8434530004
mr_scatter_plot(d_mr,d)
## $`ukb-b-20544.ukb-b-2227`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##   id.exposure id.outcome
## 1 ukb-b-20544 ukb-b-2227
d <- make_dat("ukb-b-2227", "ukb-b-20544")
## Extracting data for 3 SNP(s) from 1 GWAS(s)
## Harmonising Number of children fathered || id:ukb-b-2227 (ukb-b-2227) and Nervous feelings || id:ukb-b-20544 (ukb-b-20544)
d_mr<-mr(d)
## Analysing 'ukb-b-2227' on 'ukb-b-20544'
d_mr
##   id.exposure  id.outcome                            outcome
## 1  ukb-b-2227 ukb-b-20544 Nervous feelings || id:ukb-b-20544
## 2  ukb-b-2227 ukb-b-20544 Nervous feelings || id:ukb-b-20544
## 3  ukb-b-2227 ukb-b-20544 Nervous feelings || id:ukb-b-20544
## 4  ukb-b-2227 ukb-b-20544 Nervous feelings || id:ukb-b-20544
## 5  ukb-b-2227 ukb-b-20544 Nervous feelings || id:ukb-b-20544
##                                       exposure                    method nsnp
## 1 Number of children fathered || id:ukb-b-2227                  MR Egger    3
## 2 Number of children fathered || id:ukb-b-2227           Weighted median    3
## 3 Number of children fathered || id:ukb-b-2227 Inverse variance weighted    3
## 4 Number of children fathered || id:ukb-b-2227               Simple mode    3
## 5 Number of children fathered || id:ukb-b-2227             Weighted mode    3
##             b         se      pval
## 1 -1.31197350 3.49143631 0.7711704
## 2 -0.08390565 0.05502679 0.1273054
## 3 -0.18648445 0.14782820 0.2071307
## 4 -0.10514890 0.11138943 0.4448249
## 5 -0.01626956 0.04744864 0.7643687
mr_scatter_plot(d_mr,d)
## $`ukb-b-2227.ukb-b-20544`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##   id.exposure  id.outcome
## 1  ukb-b-2227 ukb-b-20544

Suffer from ‘nerves’

d <- make_dat("ukb-b-19957", "ukb-b-2227")
## Extracting data for 22 SNP(s) from 1 GWAS(s)
## Harmonising Suffer from 'nerves' || id:ukb-b-19957 (ukb-b-19957) and Number of children fathered || id:ukb-b-2227 (ukb-b-2227)
d_mr<-mr(d)
## Analysing 'ukb-b-19957' on 'ukb-b-2227'
d_mr
##   id.exposure id.outcome                                      outcome
## 1 ukb-b-19957 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 2 ukb-b-19957 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 3 ukb-b-19957 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 4 ukb-b-19957 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 5 ukb-b-19957 ukb-b-2227 Number of children fathered || id:ukb-b-2227
##                                 exposure                    method nsnp
## 1 Suffer from 'nerves' || id:ukb-b-19957                  MR Egger   22
## 2 Suffer from 'nerves' || id:ukb-b-19957           Weighted median   22
## 3 Suffer from 'nerves' || id:ukb-b-19957 Inverse variance weighted   22
## 4 Suffer from 'nerves' || id:ukb-b-19957               Simple mode   22
## 5 Suffer from 'nerves' || id:ukb-b-19957             Weighted mode   22
##            b        se        pval
## 1 -2.5258572 1.2491292 0.056747844
## 2 -0.2596191 0.1729880 0.133409289
## 3 -0.5929543 0.2039217 0.003640333
## 4 -0.2230810 0.3519298 0.533003861
## 5 -0.2827518 0.3688722 0.451892226
mr_scatter_plot(d_mr,d)
## $`ukb-b-19957.ukb-b-2227`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##   id.exposure id.outcome
## 1 ukb-b-19957 ukb-b-2227
d <- make_dat("ukb-b-2227", "ukb-b-19957")
## Extracting data for 3 SNP(s) from 1 GWAS(s)
## Harmonising Number of children fathered || id:ukb-b-2227 (ukb-b-2227) and Suffer from 'nerves' || id:ukb-b-19957 (ukb-b-19957)
d_mr<-mr(d)
## Analysing 'ukb-b-2227' on 'ukb-b-19957'
d_mr
##   id.exposure  id.outcome                                outcome
## 1  ukb-b-2227 ukb-b-19957 Suffer from 'nerves' || id:ukb-b-19957
## 2  ukb-b-2227 ukb-b-19957 Suffer from 'nerves' || id:ukb-b-19957
## 3  ukb-b-2227 ukb-b-19957 Suffer from 'nerves' || id:ukb-b-19957
## 4  ukb-b-2227 ukb-b-19957 Suffer from 'nerves' || id:ukb-b-19957
## 5  ukb-b-2227 ukb-b-19957 Suffer from 'nerves' || id:ukb-b-19957
##                                       exposure                    method nsnp
## 1 Number of children fathered || id:ukb-b-2227                  MR Egger    3
## 2 Number of children fathered || id:ukb-b-2227           Weighted median    3
## 3 Number of children fathered || id:ukb-b-2227 Inverse variance weighted    3
## 4 Number of children fathered || id:ukb-b-2227               Simple mode    3
## 5 Number of children fathered || id:ukb-b-2227             Weighted mode    3
##            b         se        pval
## 1 -0.9280665 2.11888898 0.737185956
## 2 -0.1544598 0.05113315 0.002521608
## 3 -0.2132529 0.09013500 0.017984933
## 4 -0.1573626 0.09010547 0.222850726
## 5 -0.1104185 0.04979204 0.156858522
mr_scatter_plot(d_mr,d)
## $`ukb-b-2227.ukb-b-19957`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##   id.exposure  id.outcome
## 1  ukb-b-2227 ukb-b-19957

Worrier / anxious feelings

d <- make_dat("ukb-b-6519", "ukb-b-2227")
## Extracting data for 67 SNP(s) from 1 GWAS(s)
## Harmonising Worrier / anxious feelings || id:ukb-b-6519 (ukb-b-6519) and Number of children fathered || id:ukb-b-2227 (ukb-b-2227)
d_mr<-mr(d)
## Analysing 'ukb-b-6519' on 'ukb-b-2227'
d_mr
##   id.exposure id.outcome                                      outcome
## 1  ukb-b-6519 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 2  ukb-b-6519 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 3  ukb-b-6519 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 4  ukb-b-6519 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 5  ukb-b-6519 ukb-b-2227 Number of children fathered || id:ukb-b-2227
##                                      exposure                    method nsnp
## 1 Worrier / anxious feelings || id:ukb-b-6519                  MR Egger   67
## 2 Worrier / anxious feelings || id:ukb-b-6519           Weighted median   67
## 3 Worrier / anxious feelings || id:ukb-b-6519 Inverse variance weighted   67
## 4 Worrier / anxious feelings || id:ukb-b-6519               Simple mode   67
## 5 Worrier / anxious feelings || id:ukb-b-6519             Weighted mode   67
##            b         se       pval
## 1 -0.3747033 0.39412312 0.34526506
## 2 -0.1691829 0.07155695 0.01806364
## 3 -0.1516209 0.07618264 0.04656574
## 4 -0.2684441 0.14526150 0.06908277
## 5 -0.2347026 0.13831807 0.09444010
mr_scatter_plot(d_mr,d)
## $`ukb-b-6519.ukb-b-2227`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##   id.exposure id.outcome
## 1  ukb-b-6519 ukb-b-2227
d <- make_dat("ukb-b-2227", "ukb-b-6519")
## Extracting data for 3 SNP(s) from 1 GWAS(s)
## Harmonising Number of children fathered || id:ukb-b-2227 (ukb-b-2227) and Worrier / anxious feelings || id:ukb-b-6519 (ukb-b-6519)
d_mr<-mr(d)
## Analysing 'ukb-b-2227' on 'ukb-b-6519'
d_mr
##   id.exposure id.outcome                                     outcome
## 1  ukb-b-2227 ukb-b-6519 Worrier / anxious feelings || id:ukb-b-6519
## 2  ukb-b-2227 ukb-b-6519 Worrier / anxious feelings || id:ukb-b-6519
## 3  ukb-b-2227 ukb-b-6519 Worrier / anxious feelings || id:ukb-b-6519
## 4  ukb-b-2227 ukb-b-6519 Worrier / anxious feelings || id:ukb-b-6519
## 5  ukb-b-2227 ukb-b-6519 Worrier / anxious feelings || id:ukb-b-6519
##                                       exposure                    method nsnp
## 1 Number of children fathered || id:ukb-b-2227                  MR Egger    3
## 2 Number of children fathered || id:ukb-b-2227           Weighted median    3
## 3 Number of children fathered || id:ukb-b-2227 Inverse variance weighted    3
## 4 Number of children fathered || id:ukb-b-2227               Simple mode    3
## 5 Number of children fathered || id:ukb-b-2227             Weighted mode    3
##            b         se       pval
## 1 -1.6038184 3.45899954 0.72360529
## 2 -0.1310460 0.06065479 0.03073232
## 3 -0.2523395 0.14966936 0.09179971
## 4 -0.1384621 0.10151538 0.30579953
## 5 -0.0786276 0.05112538 0.26390488
mr_scatter_plot(d_mr,d)
## $`ukb-b-2227.ukb-b-6519`

## 
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
##   id.exposure id.outcome
## 1  ukb-b-2227 ukb-b-6519

Maybe some evidence of a negative relationship between nerves/worry and the number of children fathered.