Investigating various mental states 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
d <- make_dat("ukb-b-18994", "ieu-b-4760")
## API: public: http://gwas-api.mrcieu.ac.uk/
## Extracting data for 48 SNP(s) from 1 GWAS(s)
## Finding proxies for 4 SNPs in outcome ieu-b-4760
## Extracting data for 4 SNP(s) from 1 GWAS(s)
## Harmonising Miserableness || id:ukb-b-18994 (ukb-b-18994) and Number of children || id:ieu-b-4760 (ieu-b-4760)
d_mr<-mr(d)
## Analysing 'ukb-b-18994' on 'ieu-b-4760'
d_mr
## id.exposure id.outcome outcome
## 1 ukb-b-18994 ieu-b-4760 Number of children || id:ieu-b-4760
## 2 ukb-b-18994 ieu-b-4760 Number of children || id:ieu-b-4760
## 3 ukb-b-18994 ieu-b-4760 Number of children || id:ieu-b-4760
## 4 ukb-b-18994 ieu-b-4760 Number of children || id:ieu-b-4760
## 5 ukb-b-18994 ieu-b-4760 Number of children || id:ieu-b-4760
## exposure method nsnp b
## 1 Miserableness || id:ukb-b-18994 MR Egger 90 0.30010557
## 2 Miserableness || id:ukb-b-18994 Weighted median 90 0.08272921
## 3 Miserableness || id:ukb-b-18994 Inverse variance weighted 90 0.10868011
## 4 Miserableness || id:ukb-b-18994 Simple mode 90 0.33244297
## 5 Miserableness || id:ukb-b-18994 Weighted mode 90 0.31914523
## se pval
## 1 0.22465820 0.18504876
## 2 0.05475258 0.13079747
## 3 0.05259735 0.03880340
## 4 0.17250369 0.05714904
## 5 0.16071720 0.05013807
mr_scatter_plot(d_mr,d)
## $`ukb-b-18994.ieu-b-4760`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-18994 ieu-b-4760
d <- make_dat("ieu-b-4760", "ukb-b-18994")
## Warning in .fun(piece, ...): Duplicated SNPs present in exposure data for phenotype 'Number of children || id:ieu-b-4760. Just keeping the first instance:
## rs6800021
## rs6782190
## rs4870063
## rs10270358
## rs201945769
## rs2360806
## rs72687493
## rs62054570
## rs2957316
## Extracting data for 9 SNP(s) from 1 GWAS(s)
## Finding proxies for 1 SNPs in outcome ukb-b-18994
## Extracting data for 1 SNP(s) from 1 GWAS(s)
## Harmonising Number of children || id:ieu-b-4760 (ieu-b-4760) and Miserableness || id:ukb-b-18994 (ukb-b-18994)
d_mr<-mr(d)
## Analysing 'ieu-b-4760' on 'ukb-b-18994'
d_mr
## id.exposure id.outcome outcome
## 1 ieu-b-4760 ukb-b-18994 Miserableness || id:ukb-b-18994
## 2 ieu-b-4760 ukb-b-18994 Miserableness || id:ukb-b-18994
## 3 ieu-b-4760 ukb-b-18994 Miserableness || id:ukb-b-18994
## 4 ieu-b-4760 ukb-b-18994 Miserableness || id:ukb-b-18994
## 5 ieu-b-4760 ukb-b-18994 Miserableness || id:ukb-b-18994
## exposure method nsnp
## 1 Number of children || id:ieu-b-4760 MR Egger 8
## 2 Number of children || id:ieu-b-4760 Weighted median 8
## 3 Number of children || id:ieu-b-4760 Inverse variance weighted 8
## 4 Number of children || id:ieu-b-4760 Simple mode 8
## 5 Number of children || id:ieu-b-4760 Weighted mode 8
## b se pval
## 1 -0.47200736 0.44333357 0.3279802
## 2 -0.02905840 0.03956855 0.4627163
## 3 0.07222224 0.07990465 0.3660721
## 4 -0.03545515 0.04289482 0.4357511
## 5 -0.03803850 0.03782142 0.3480335
mr_scatter_plot(d_mr,d)
## $`ieu-b-4760.ukb-b-18994`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ieu-b-4760 ukb-b-18994
d <- make_dat("ukb-b-5664", "ieu-b-4760")
## Extracting data for 18 SNP(s) from 1 GWAS(s)
## Finding proxies for 2 SNPs in outcome ieu-b-4760
## Extracting data for 2 SNP(s) from 1 GWAS(s)
## Harmonising Frequency of tenseness / restlessness in last 2 weeks || id:ukb-b-5664 (ukb-b-5664) and Number of children || id:ieu-b-4760 (ieu-b-4760)
d_mr<-mr(d)
## Analysing 'ukb-b-5664' on 'ieu-b-4760'
d_mr
## id.exposure id.outcome outcome
## 1 ukb-b-5664 ieu-b-4760 Number of children || id:ieu-b-4760
## 2 ukb-b-5664 ieu-b-4760 Number of children || id:ieu-b-4760
## 3 ukb-b-5664 ieu-b-4760 Number of children || id:ieu-b-4760
## 4 ukb-b-5664 ieu-b-4760 Number of children || id:ieu-b-4760
## 5 ukb-b-5664 ieu-b-4760 Number of children || id:ieu-b-4760
## exposure
## 1 Frequency of tenseness / restlessness in last 2 weeks || id:ukb-b-5664
## 2 Frequency of tenseness / restlessness in last 2 weeks || id:ukb-b-5664
## 3 Frequency of tenseness / restlessness in last 2 weeks || id:ukb-b-5664
## 4 Frequency of tenseness / restlessness in last 2 weeks || id:ukb-b-5664
## 5 Frequency of tenseness / restlessness in last 2 weeks || id:ukb-b-5664
## method nsnp b se pval
## 1 MR Egger 32 0.51267913 0.27835221 7.540501e-02
## 2 Weighted median 32 0.17293536 0.08116792 3.312314e-02
## 3 Inverse variance weighted 32 0.31999987 0.07788704 3.982162e-05
## 4 Simple mode 32 0.02800112 0.16790745 8.686378e-01
## 5 Weighted mode 32 0.04896937 0.14748215 7.420968e-01
mr_scatter_plot(d_mr,d)
## $`ukb-b-5664.ieu-b-4760`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-5664 ieu-b-4760
d <- make_dat("ieu-b-4760", "ukb-b-5664")
## Warning in .fun(piece, ...): Duplicated SNPs present in exposure data for phenotype 'Number of children || id:ieu-b-4760. Just keeping the first instance:
## rs6800021
## rs6782190
## rs4870063
## rs10270358
## rs201945769
## rs2360806
## rs72687493
## rs62054570
## rs2957316
## Extracting data for 9 SNP(s) from 1 GWAS(s)
## Finding proxies for 1 SNPs in outcome ukb-b-5664
## Extracting data for 1 SNP(s) from 1 GWAS(s)
## Harmonising Number of children || id:ieu-b-4760 (ieu-b-4760) and Frequency of tenseness / restlessness in last 2 weeks || id:ukb-b-5664 (ukb-b-5664)
d_mr<-mr(d)
## Analysing 'ieu-b-4760' on 'ukb-b-5664'
d_mr
## id.exposure id.outcome
## 1 ieu-b-4760 ukb-b-5664
## 2 ieu-b-4760 ukb-b-5664
## 3 ieu-b-4760 ukb-b-5664
## 4 ieu-b-4760 ukb-b-5664
## 5 ieu-b-4760 ukb-b-5664
## outcome
## 1 Frequency of tenseness / restlessness in last 2 weeks || id:ukb-b-5664
## 2 Frequency of tenseness / restlessness in last 2 weeks || id:ukb-b-5664
## 3 Frequency of tenseness / restlessness in last 2 weeks || id:ukb-b-5664
## 4 Frequency of tenseness / restlessness in last 2 weeks || id:ukb-b-5664
## 5 Frequency of tenseness / restlessness in last 2 weeks || id:ukb-b-5664
## exposure method nsnp
## 1 Number of children || id:ieu-b-4760 MR Egger 8
## 2 Number of children || id:ieu-b-4760 Weighted median 8
## 3 Number of children || id:ieu-b-4760 Inverse variance weighted 8
## 4 Number of children || id:ieu-b-4760 Simple mode 8
## 5 Number of children || id:ieu-b-4760 Weighted mode 8
## b se pval
## 1 -0.34006996 0.57319563 0.5746556
## 2 -0.02473377 0.04840624 0.6093774
## 3 0.09922668 0.09660719 0.3043664
## 4 -0.01247104 0.07274713 0.8687361
## 5 -0.02256278 0.05197656 0.6772847
mr_scatter_plot(d_mr,d)
## $`ieu-b-4760.ukb-b-5664`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ieu-b-4760 ukb-b-5664
Noisy measures, not much evidence of a consistent effect.