Investigating activity measures 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
d <- make_dat("ukb-b-969", "ukb-b-2227")
## API: public: http://gwas-api.mrcieu.ac.uk/
## Extracting data for 47 SNP(s) from 1 GWAS(s)
## Harmonising Time spend outdoors in summer || id:ukb-b-969 (ukb-b-969) and Number of children fathered || id:ukb-b-2227 (ukb-b-2227)
d_mr<-mr(d)
## Analysing 'ukb-b-969' on 'ukb-b-2227'
d_mr
## id.exposure id.outcome outcome
## 1 ukb-b-969 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 2 ukb-b-969 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 3 ukb-b-969 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 4 ukb-b-969 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 5 ukb-b-969 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## exposure method nsnp
## 1 Time spend outdoors in summer || id:ukb-b-969 MR Egger 47
## 2 Time spend outdoors in summer || id:ukb-b-969 Weighted median 47
## 3 Time spend outdoors in summer || id:ukb-b-969 Inverse variance weighted 47
## 4 Time spend outdoors in summer || id:ukb-b-969 Simple mode 47
## 5 Time spend outdoors in summer || id:ukb-b-969 Weighted mode 47
## b se pval
## 1 -0.2006888 0.24815489 4.229291e-01
## 2 0.1564589 0.04876532 1.334736e-03
## 3 0.2144585 0.05073893 2.371379e-05
## 4 0.1798285 0.10519222 9.409292e-02
## 5 0.1749225 0.07793433 2.965371e-02
mr_scatter_plot(d_mr,d)
## $`ukb-b-969.ukb-b-2227`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-969 ukb-b-2227
d <- make_dat("ukb-b-2227", "ukb-b-969")
## Extracting data for 3 SNP(s) from 1 GWAS(s)
## Harmonising Number of children fathered || id:ukb-b-2227 (ukb-b-2227) and Time spend outdoors in summer || id:ukb-b-969 (ukb-b-969)
d_mr<-mr(d)
## Analysing 'ukb-b-2227' on 'ukb-b-969'
d_mr
## id.exposure id.outcome outcome
## 1 ukb-b-2227 ukb-b-969 Time spend outdoors in summer || id:ukb-b-969
## 2 ukb-b-2227 ukb-b-969 Time spend outdoors in summer || id:ukb-b-969
## 3 ukb-b-2227 ukb-b-969 Time spend outdoors in summer || id:ukb-b-969
## 4 ukb-b-2227 ukb-b-969 Time spend outdoors in summer || id:ukb-b-969
## 5 ukb-b-2227 ukb-b-969 Time spend outdoors in summer || id:ukb-b-969
## 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 2.94690695 5.8452787 0.7027219
## 2 0.08725469 0.1163107 0.4531424
## 3 0.28198324 0.2589522 0.2761807
## 4 0.03859067 0.1497895 0.8207758
## 5 -0.01029508 0.0968519 0.9250480
mr_scatter_plot(d_mr,d)
## $`ukb-b-2227.ukb-b-969`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-2227 ukb-b-969
d <- make_dat("ukb-b-4549", "ukb-b-2227")
## Extracting data for 25 SNP(s) from 1 GWAS(s)
## Harmonising Drive faster than motorway speed limit || id:ukb-b-4549 (ukb-b-4549) and Number of children fathered || id:ukb-b-2227 (ukb-b-2227)
d_mr<-mr(d)
## Analysing 'ukb-b-4549' on 'ukb-b-2227'
d_mr
## id.exposure id.outcome outcome
## 1 ukb-b-4549 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 2 ukb-b-4549 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 3 ukb-b-4549 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 4 ukb-b-4549 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 5 ukb-b-4549 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## exposure
## 1 Drive faster than motorway speed limit || id:ukb-b-4549
## 2 Drive faster than motorway speed limit || id:ukb-b-4549
## 3 Drive faster than motorway speed limit || id:ukb-b-4549
## 4 Drive faster than motorway speed limit || id:ukb-b-4549
## 5 Drive faster than motorway speed limit || id:ukb-b-4549
## method nsnp b se pval
## 1 MR Egger 25 0.8952530 0.42044752 0.044155764
## 2 Weighted median 25 0.2532436 0.07353085 0.000573078
## 3 Inverse variance weighted 25 0.2933544 0.09152864 0.001350363
## 4 Simple mode 25 0.2406209 0.12899141 0.074396255
## 5 Weighted mode 25 0.2460415 0.12821070 0.066946862
mr_scatter_plot(d_mr,d)
## $`ukb-b-4549.ukb-b-2227`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-4549 ukb-b-2227
d <- make_dat("ukb-b-2227", "ukb-b-4549")
## Extracting data for 3 SNP(s) from 1 GWAS(s)
## Harmonising Number of children fathered || id:ukb-b-2227 (ukb-b-2227) and Drive faster than motorway speed limit || id:ukb-b-4549 (ukb-b-4549)
d_mr<-mr(d)
## Analysing 'ukb-b-2227' on 'ukb-b-4549'
d_mr
## id.exposure id.outcome
## 1 ukb-b-2227 ukb-b-4549
## 2 ukb-b-2227 ukb-b-4549
## 3 ukb-b-2227 ukb-b-4549
## 4 ukb-b-2227 ukb-b-4549
## 5 ukb-b-2227 ukb-b-4549
## outcome
## 1 Drive faster than motorway speed limit || id:ukb-b-4549
## 2 Drive faster than motorway speed limit || id:ukb-b-4549
## 3 Drive faster than motorway speed limit || id:ukb-b-4549
## 4 Drive faster than motorway speed limit || id:ukb-b-4549
## 5 Drive faster than motorway speed limit || id:ukb-b-4549
## 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 2.837100582 7.44148524 0.7681158
## 2 0.124462423 0.09862655 0.2069644
## 3 0.345771039 0.31634707 0.2743887
## 4 0.155120192 0.22941707 0.5686555
## 5 -0.003328508 0.08573307 0.9725576
mr_scatter_plot(d_mr,d)
## $`ukb-b-2227.ukb-b-4549`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-2227 ukb-b-4549
Both time spent outdoors in summer and driving faster than the motorway speed limit seem to be positively related to the number of children fathered.