Investigating sexual behaviour 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-6591", "ukb-b-2227")
## API: public: http://gwas-api.mrcieu.ac.uk/
## Extracting data for 200 SNP(s) from 1 GWAS(s)
## Harmonising Age first had sexual intercourse || id:ukb-b-6591 (ukb-b-6591) and Number of children fathered || id:ukb-b-2227 (ukb-b-2227)
d_mr<-mr(d)
## Analysing 'ukb-b-6591' on 'ukb-b-2227'
d_mr
## id.exposure id.outcome outcome
## 1 ukb-b-6591 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 2 ukb-b-6591 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 3 ukb-b-6591 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 4 ukb-b-6591 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 5 ukb-b-6591 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## exposure method
## 1 Age first had sexual intercourse || id:ukb-b-6591 MR Egger
## 2 Age first had sexual intercourse || id:ukb-b-6591 Weighted median
## 3 Age first had sexual intercourse || id:ukb-b-6591 Inverse variance weighted
## 4 Age first had sexual intercourse || id:ukb-b-6591 Simple mode
## 5 Age first had sexual intercourse || id:ukb-b-6591 Weighted mode
## nsnp b se pval
## 1 200 -0.2323828 0.06538964 4.747170e-04
## 2 200 -0.1339094 0.01891551 1.448400e-12
## 3 200 -0.1162577 0.01473031 2.963927e-15
## 4 200 -0.1460973 0.05434631 7.791079e-03
## 5 200 -0.1556233 0.05158895 2.889900e-03
mr_scatter_plot(d_mr,d)
## $`ukb-b-6591.ukb-b-2227`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-6591 ukb-b-2227
d <- make_dat("ukb-b-2227", "ukb-b-6591")
## Extracting data for 3 SNP(s) from 1 GWAS(s)
## Harmonising Number of children fathered || id:ukb-b-2227 (ukb-b-2227) and Age first had sexual intercourse || id:ukb-b-6591 (ukb-b-6591)
d_mr<-mr(d)
## Analysing 'ukb-b-2227' on 'ukb-b-6591'
d_mr
## id.exposure id.outcome outcome
## 1 ukb-b-2227 ukb-b-6591 Age first had sexual intercourse || id:ukb-b-6591
## 2 ukb-b-2227 ukb-b-6591 Age first had sexual intercourse || id:ukb-b-6591
## 3 ukb-b-2227 ukb-b-6591 Age first had sexual intercourse || id:ukb-b-6591
## 4 ukb-b-2227 ukb-b-6591 Age first had sexual intercourse || id:ukb-b-6591
## 5 ukb-b-2227 ukb-b-6591 Age first had sexual intercourse || id:ukb-b-6591
## 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 -7.2979991 6.35619662 0.45615839
## 2 -0.1991806 0.10968546 0.06938188
## 3 -0.6044164 0.37230673 0.10449608
## 4 -0.1462293 0.10562465 0.30045949
## 5 -0.1632583 0.09529786 0.22882025
mr_scatter_plot(d_mr,d)
## $`ukb-b-2227.ukb-b-6591`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-2227 ukb-b-6591
Very highly related
d <- make_dat("ukb-b-4256", "ukb-b-2227")
## Extracting data for 63 SNP(s) from 1 GWAS(s)
## Harmonising Lifetime number of sexual partners || id:ukb-b-4256 (ukb-b-4256) and Number of children fathered || id:ukb-b-2227 (ukb-b-2227)
d_mr<-mr(d)
## Analysing 'ukb-b-4256' on 'ukb-b-2227'
d_mr
## id.exposure id.outcome outcome
## 1 ukb-b-4256 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 2 ukb-b-4256 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 3 ukb-b-4256 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 4 ukb-b-4256 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 5 ukb-b-4256 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## exposure method
## 1 Lifetime number of sexual partners || id:ukb-b-4256 MR Egger
## 2 Lifetime number of sexual partners || id:ukb-b-4256 Weighted median
## 3 Lifetime number of sexual partners || id:ukb-b-4256 Inverse variance weighted
## 4 Lifetime number of sexual partners || id:ukb-b-4256 Simple mode
## 5 Lifetime number of sexual partners || id:ukb-b-4256 Weighted mode
## nsnp b se pval
## 1 63 0.16056366 0.22711402 0.4822748
## 2 63 -0.04904491 0.04278337 0.2516485
## 3 63 -0.03196317 0.04880948 0.5125607
## 4 63 -0.02021716 0.11489113 0.8608926
## 5 63 -0.02701496 0.10995438 0.8067318
mr_scatter_plot(d_mr,d)
## $`ukb-b-4256.ukb-b-2227`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-4256 ukb-b-2227
d <- make_dat("ukb-b-2227", "ukb-b-4256")
## Extracting data for 3 SNP(s) from 1 GWAS(s)
## Harmonising Number of children fathered || id:ukb-b-2227 (ukb-b-2227) and Lifetime number of sexual partners || id:ukb-b-4256 (ukb-b-4256)
d_mr<-mr(d)
## Analysing 'ukb-b-2227' on 'ukb-b-4256'
d_mr
## id.exposure id.outcome outcome
## 1 ukb-b-2227 ukb-b-4256 Lifetime number of sexual partners || id:ukb-b-4256
## 2 ukb-b-2227 ukb-b-4256 Lifetime number of sexual partners || id:ukb-b-4256
## 3 ukb-b-2227 ukb-b-4256 Lifetime number of sexual partners || id:ukb-b-4256
## 4 ukb-b-2227 ukb-b-4256 Lifetime number of sexual partners || id:ukb-b-4256
## 5 ukb-b-2227 ukb-b-4256 Lifetime number of sexual partners || id:ukb-b-4256
## 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 4.91957753 8.0524246 0.65086024
## 2 -0.25245784 0.1162149 0.02983031
## 3 0.07777055 0.3789532 0.83739660
## 4 -0.34530809 0.1019036 0.07714630
## 5 -0.35546812 0.1055269 0.07796317
mr_scatter_plot(d_mr,d)
## $`ukb-b-2227.ukb-b-4256`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-2227 ukb-b-4256
No impact.