Metabolites and proteins
Clare Horscroft
05/08/2021
Investigating metabolites and proteins in relation to number of children
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 detailsMetabolites
Docosahexaenoic acid
d <- make_dat("met-d-DHA", "ieu-b-4760")## API: public: http://gwas-api.mrcieu.ac.uk/## Extracting data for 48 SNP(s) from 1 GWAS(s)## Finding proxies for 15 SNPs in outcome ieu-b-4760## Extracting data for 15 SNP(s) from 1 GWAS(s)## Harmonising Docosahexaenoic acid || id:met-d-DHA (met-d-DHA) and Number of children || id:ieu-b-4760 (ieu-b-4760)d_mr<-mr(d)## Analysing 'met-d-DHA' on 'ieu-b-4760'd_mr## id.exposure id.outcome outcome
## 1 met-d-DHA ieu-b-4760 Number of children || id:ieu-b-4760
## 2 met-d-DHA ieu-b-4760 Number of children || id:ieu-b-4760
## 3 met-d-DHA ieu-b-4760 Number of children || id:ieu-b-4760
## 4 met-d-DHA ieu-b-4760 Number of children || id:ieu-b-4760
## 5 met-d-DHA ieu-b-4760 Number of children || id:ieu-b-4760
## exposure method nsnp
## 1 Docosahexaenoic acid || id:met-d-DHA MR Egger 42
## 2 Docosahexaenoic acid || id:met-d-DHA Weighted median 42
## 3 Docosahexaenoic acid || id:met-d-DHA Inverse variance weighted 42
## 4 Docosahexaenoic acid || id:met-d-DHA Simple mode 42
## 5 Docosahexaenoic acid || id:met-d-DHA Weighted mode 42
## b se pval
## 1 0.036014869 0.010937273 2.079883e-03
## 2 0.029864425 0.006705460 8.438427e-06
## 3 0.013711298 0.008317863 9.926734e-02
## 4 -0.005220384 0.021398431 8.084777e-01
## 5 0.030317469 0.006479307 3.128449e-05mr_scatter_plot(d_mr,d)## $`met-d-DHA.ieu-b-4760`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 met-d-DHA ieu-b-4760d <- make_dat("ieu-b-4760", "met-d-DHA")## Extracting data for 9 SNP(s) from 1 GWAS(s)## Finding proxies for 1 SNPs in outcome met-d-DHA## Extracting data for 1 SNP(s) from 1 GWAS(s)## Harmonising Number of children || id:ieu-b-4760 (ieu-b-4760) and Docosahexaenoic acid || id:met-d-DHA (met-d-DHA)d_mr<-mr(d)## Analysing 'ieu-b-4760' on 'met-d-DHA'd_mr## id.exposure id.outcome outcome
## 1 ieu-b-4760 met-d-DHA Docosahexaenoic acid || id:met-d-DHA
## 2 ieu-b-4760 met-d-DHA Docosahexaenoic acid || id:met-d-DHA
## 3 ieu-b-4760 met-d-DHA Docosahexaenoic acid || id:met-d-DHA
## 4 ieu-b-4760 met-d-DHA Docosahexaenoic acid || id:met-d-DHA
## 5 ieu-b-4760 met-d-DHA Docosahexaenoic acid || id:met-d-DHA
## exposure method nsnp b
## 1 Number of children || id:ieu-b-4760 MR Egger 8 0.6400589
## 2 Number of children || id:ieu-b-4760 Weighted median 8 0.1659552
## 3 Number of children || id:ieu-b-4760 Inverse variance weighted 8 -0.1116705
## 4 Number of children || id:ieu-b-4760 Simple mode 8 0.1822140
## 5 Number of children || id:ieu-b-4760 Weighted mode 8 0.2026140
## se pval
## 1 1.7590578 0.7284369
## 2 0.1346900 0.2179015
## 3 0.2869383 0.6971435
## 4 0.1684099 0.3151250
## 5 0.1653433 0.2600458mr_scatter_plot(d_mr,d)## $`ieu-b-4760.met-d-DHA`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ieu-b-4760 met-d-DHARatio of docosahexaenoic acid to total fatty acids
d <- make_dat("met-d-DHA_pct", "ieu-b-4760")## Extracting data for 28 SNP(s) from 1 GWAS(s)## Finding proxies for 5 SNPs in outcome ieu-b-4760## Extracting data for 5 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 children || id:ieu-b-4760 (ieu-b-4760)d_mr<-mr(d)## Analysing 'met-d-DHA_pct' on 'ieu-b-4760'd_mr## id.exposure id.outcome outcome
## 1 met-d-DHA_pct ieu-b-4760 Number of children || id:ieu-b-4760
## 2 met-d-DHA_pct ieu-b-4760 Number of children || id:ieu-b-4760
## 3 met-d-DHA_pct ieu-b-4760 Number of children || id:ieu-b-4760
## 4 met-d-DHA_pct ieu-b-4760 Number of children || id:ieu-b-4760
## 5 met-d-DHA_pct ieu-b-4760 Number of children || id:ieu-b-4760
## 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 27 0.04286676 0.013210248 3.327539e-03
## 2 Weighted median 27 0.03438251 0.007600403 6.074632e-06
## 3 Inverse variance weighted 27 0.01969161 0.010331030 5.664176e-02
## 4 Simple mode 27 0.02189154 0.024237102 3.746995e-01
## 5 Weighted mode 27 0.03248531 0.007097507 1.026696e-04mr_scatter_plot(d_mr,d)## $`met-d-DHA_pct.ieu-b-4760`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 met-d-DHA_pct ieu-b-4760d <- make_dat("ieu-b-4760", "met-d-DHA_pct")## Extracting data for 9 SNP(s) from 1 GWAS(s)## Finding proxies for 1 SNPs in outcome met-d-DHA_pct## Extracting data for 1 SNP(s) from 1 GWAS(s)## Harmonising Number of children || id:ieu-b-4760 (ieu-b-4760) and Ratio of docosahexaenoic acid to total fatty acids || id:met-d-DHA_pct (met-d-DHA_pct)d_mr<-mr(d)## Analysing 'ieu-b-4760' on 'met-d-DHA_pct'd_mr## id.exposure id.outcome
## 1 ieu-b-4760 met-d-DHA_pct
## 2 ieu-b-4760 met-d-DHA_pct
## 3 ieu-b-4760 met-d-DHA_pct
## 4 ieu-b-4760 met-d-DHA_pct
## 5 ieu-b-4760 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 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 1.30257154 1.7365375 0.4815636
## 2 0.09661264 0.1544789 0.5317019
## 3 -0.17678660 0.2957963 0.5500646
## 4 -0.08063977 0.2243023 0.7298117
## 5 0.22506506 0.1852153 0.2636982mr_scatter_plot(d_mr,d)## $`ieu-b-4760.met-d-DHA_pct`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ieu-b-4760 met-d-DHA_pctSeems 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", "ieu-b-4760")## Extracting data for 41 SNP(s) from 1 GWAS(s)## Finding proxies for 9 SNPs in outcome ieu-b-4760## Extracting data for 9 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 children || id:ieu-b-4760 (ieu-b-4760)d_mr<-mr(d)## Analysing 'met-d-Omega_3_pct' on 'ieu-b-4760'd_mr## id.exposure id.outcome outcome
## 1 met-d-Omega_3_pct ieu-b-4760 Number of children || id:ieu-b-4760
## 2 met-d-Omega_3_pct ieu-b-4760 Number of children || id:ieu-b-4760
## 3 met-d-Omega_3_pct ieu-b-4760 Number of children || id:ieu-b-4760
## 4 met-d-Omega_3_pct ieu-b-4760 Number of children || id:ieu-b-4760
## 5 met-d-Omega_3_pct ieu-b-4760 Number of children || id:ieu-b-4760
## 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 38 0.02925668 0.006689168 9.993115e-05
## 2 Weighted median 38 0.02437907 0.005292407 4.096525e-06
## 3 Inverse variance weighted 38 0.01387771 0.006131432 2.361282e-02
## 4 Simple mode 38 -0.01010978 0.022418104 6.546468e-01
## 5 Weighted mode 38 0.02390575 0.005460928 9.458495e-05mr_scatter_plot(d_mr,d)## $`met-d-Omega_3_pct.ieu-b-4760`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 met-d-Omega_3_pct ieu-b-4760d <- make_dat("ieu-b-4760", "met-d-Omega_3_pct")## Extracting data for 9 SNP(s) from 1 GWAS(s)## Finding proxies for 1 SNPs in outcome met-d-Omega_3_pct## Extracting data for 1 SNP(s) from 1 GWAS(s)## Harmonising Number of children || id:ieu-b-4760 (ieu-b-4760) 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 'ieu-b-4760' on 'met-d-Omega_3_pct'd_mr## id.exposure id.outcome
## 1 ieu-b-4760 met-d-Omega_3_pct
## 2 ieu-b-4760 met-d-Omega_3_pct
## 3 ieu-b-4760 met-d-Omega_3_pct
## 4 ieu-b-4760 met-d-Omega_3_pct
## 5 ieu-b-4760 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 b
## 1 Number of children || id:ieu-b-4760 MR Egger 8 0.6419761
## 2 Number of children || id:ieu-b-4760 Weighted median 8 0.2786102
## 3 Number of children || id:ieu-b-4760 Inverse variance weighted 8 -0.0902219
## 4 Number of children || id:ieu-b-4760 Simple mode 8 0.2739892
## 5 Number of children || id:ieu-b-4760 Weighted mode 8 0.2819510
## se pval
## 1 2.0002045 0.75912930
## 2 0.1445370 0.05390436
## 3 0.3249299 0.78126896
## 4 0.1738415 0.15900992
## 5 0.1515907 0.10521941mr_scatter_plot(d_mr,d)## $`ieu-b-4760.met-d-Omega_3_pct`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ieu-b-4760 met-d-Omega_3_pctRatio of omega-6 fatty acids to omega-3 fatty acids
d <- make_dat("met-d-Omega_6_by_Omega_3", "ieu-b-4760")## Extracting data for 41 SNP(s) from 1 GWAS(s)## Finding proxies for 11 SNPs in outcome ieu-b-4760## Extracting data for 11 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 children || id:ieu-b-4760 (ieu-b-4760)d_mr<-mr(d)## Analysing 'met-d-Omega_6_by_Omega_3' on 'ieu-b-4760'd_mr## id.exposure id.outcome outcome
## 1 met-d-Omega_6_by_Omega_3 ieu-b-4760 Number of children || id:ieu-b-4760
## 2 met-d-Omega_6_by_Omega_3 ieu-b-4760 Number of children || id:ieu-b-4760
## 3 met-d-Omega_6_by_Omega_3 ieu-b-4760 Number of children || id:ieu-b-4760
## 4 met-d-Omega_6_by_Omega_3 ieu-b-4760 Number of children || id:ieu-b-4760
## 5 met-d-Omega_6_by_Omega_3 ieu-b-4760 Number of children || id:ieu-b-4760
## 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 37 -0.029448191 0.007990564 7.674472e-04
## 2 Weighted median 37 -0.024477980 0.005670536 1.583818e-05
## 3 Inverse variance weighted 37 -0.013517297 0.006762964 4.563826e-02
## 4 Simple mode 37 0.005415459 0.020296991 7.911372e-01
## 5 Weighted mode 37 -0.024766576 0.005478273 6.429281e-05mr_scatter_plot(d_mr,d)## $`met-d-Omega_6_by_Omega_3.ieu-b-4760`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 met-d-Omega_6_by_Omega_3 ieu-b-4760d <- make_dat("ieu-b-4760", "met-d-Omega_6_by_Omega_3")## Extracting data for 9 SNP(s) from 1 GWAS(s)## Finding proxies for 1 SNPs in outcome met-d-Omega_6_by_Omega_3## Extracting data for 1 SNP(s) from 1 GWAS(s)## Harmonising Number of children || id:ieu-b-4760 (ieu-b-4760) 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 'ieu-b-4760' on 'met-d-Omega_6_by_Omega_3'd_mr## id.exposure id.outcome
## 1 ieu-b-4760 met-d-Omega_6_by_Omega_3
## 2 ieu-b-4760 met-d-Omega_6_by_Omega_3
## 3 ieu-b-4760 met-d-Omega_6_by_Omega_3
## 4 ieu-b-4760 met-d-Omega_6_by_Omega_3
## 5 ieu-b-4760 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 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 -0.36270837 2.0362274 0.8644847
## 2 -0.21596454 0.1461986 0.1396221
## 3 0.03850972 0.3281091 0.9065679
## 4 -0.24636466 0.1926627 0.2417497
## 5 -0.25489600 0.1640552 0.1641972mr_scatter_plot(d_mr,d)## $`ieu-b-4760.met-d-Omega_6_by_Omega_3`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ieu-b-4760 met-d-Omega_6_by_Omega_3Omega 3 related measures appears to be related to number of children.
d <- mv_extract_exposures(c("met-d-DHA_pct", "met-d-Omega_3_pct"))## Please look at vignettes for options on running this locally if you need to run many instances of this command.## Clumping 1, 57 variants, using EUR population reference## Removing 13 of 57 variants due to LD with other variants or absence from LD reference panel## Extracting data for 44 SNP(s) from 2 GWAS(s)## Harmonising Ratio of docosahexaenoic acid to total fatty acids || id:met-d-DHA_pct (met-d-DHA_pct) and Ratio of omega-3 fatty acids to total fatty acids || id:met-d-Omega_3_pct (met-d-Omega_3_pct)o <- extract_outcome_data(d$SNP, "ieu-b-4760")## Extracting data for 44 SNP(s) from 1 GWAS(s)## Finding proxies for 10 SNPs in outcome ieu-b-4760## Extracting data for 10 SNP(s) from 1 GWAS(s)d <- mv_harmonise_data(d, o)## Harmonising Ratio of docosahexaenoic acid to total fatty acids || id:met-d-DHA_pct (met-d-DHA_pct) and Number of children || id:ieu-b-4760 (ieu-b-4760)mv_multiple(d)## $result
## id.exposure
## 1 met-d-DHA_pct
## 2 met-d-Omega_3_pct
## exposure
## 1 Ratio of docosahexaenoic acid to total fatty acids || id:met-d-DHA_pct
## 2 Ratio of omega-3 fatty acids to total fatty acids || id:met-d-Omega_3_pct
## id.outcome outcome nsnp b se
## 1 ieu-b-4760 Number of children || id:ieu-b-4760 23 0.014842856 0.0189216
## 2 ieu-b-4760 Number of children || id:ieu-b-4760 34 0.004200415 0.0139937
## pval
## 1 0.4327821
## 2 0.7640516What does this mean??
Proteins
Both proteins have very small sample sizes <4000. There may be a relation between these proteins and number of children,
Erythrocyte band 7 integral membrane protein
d <- make_dat("prot-a-2882", "ieu-b-4760")## Extracting data for 1 SNP(s) from 1 GWAS(s)## Harmonising Erythrocyte band 7 integral membrane protein || id:prot-a-2882 (prot-a-2882) and Number of children || id:ieu-b-4760 (ieu-b-4760)d_mr<-mr(d)## Analysing 'prot-a-2882' on 'ieu-b-4760'd_mr## id.exposure id.outcome outcome
## 1 prot-a-2882 ieu-b-4760 Number of children || id:ieu-b-4760
## exposure method
## 1 Erythrocyte band 7 integral membrane protein || id:prot-a-2882 Wald ratio
## nsnp b se pval
## 1 1 0.01267427 0.004647233 0.006386023mr_scatter_plot(d_mr,d)## $`prot-a-2882.ieu-b-4760`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 prot-a-2882 ieu-b-4760d <- make_dat("ieu-b-4760", "prot-a-2882")## Extracting data for 9 SNP(s) from 1 GWAS(s)## Finding proxies for 2 SNPs in outcome prot-a-2882## Extracting data for 2 SNP(s) from 1 GWAS(s)## Harmonising Number of children || id:ieu-b-4760 (ieu-b-4760) and Erythrocyte band 7 integral membrane protein || id:prot-a-2882 (prot-a-2882)d_mr<-mr(d)## Analysing 'ieu-b-4760' on 'prot-a-2882'd_mr## id.exposure id.outcome
## 1 ieu-b-4760 prot-a-2882
## 2 ieu-b-4760 prot-a-2882
## 3 ieu-b-4760 prot-a-2882
## 4 ieu-b-4760 prot-a-2882
## 5 ieu-b-4760 prot-a-2882
## outcome
## 1 Erythrocyte band 7 integral membrane protein || id:prot-a-2882
## 2 Erythrocyte band 7 integral membrane protein || id:prot-a-2882
## 3 Erythrocyte band 7 integral membrane protein || id:prot-a-2882
## 4 Erythrocyte band 7 integral membrane protein || id:prot-a-2882
## 5 Erythrocyte band 7 integral membrane protein || id:prot-a-2882
## exposure method nsnp
## 1 Number of children || id:ieu-b-4760 MR Egger 7
## 2 Number of children || id:ieu-b-4760 Weighted median 7
## 3 Number of children || id:ieu-b-4760 Inverse variance weighted 7
## 4 Number of children || id:ieu-b-4760 Simple mode 7
## 5 Number of children || id:ieu-b-4760 Weighted mode 7
## b se pval
## 1 -15.4409122 9.0057642 0.1470901
## 2 -0.4518077 0.9384447 0.6302017
## 3 1.2443795 1.9413299 0.5215270
## 4 -0.2529567 1.1359525 0.8311697
## 5 -0.7008984 1.0583611 0.5324091mr_scatter_plot(d_mr,d)## $`ieu-b-4760.prot-a-2882`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ieu-b-4760 prot-a-2882Transmembrane protease serine 11D
d <- make_dat("prot-a-3024", "ieu-b-4760")## Extracting data for 1 SNP(s) from 1 GWAS(s)## Harmonising Transmembrane protease serine 11D || id:prot-a-3024 (prot-a-3024) and Number of children || id:ieu-b-4760 (ieu-b-4760)d_mr<-mr(d)## Analysing 'prot-a-3024' on 'ieu-b-4760'd_mr## id.exposure id.outcome outcome
## 1 prot-a-3024 ieu-b-4760 Number of children || id:ieu-b-4760
## exposure method nsnp
## 1 Transmembrane protease serine 11D || id:prot-a-3024 Wald ratio 1
## b se pval
## 1 0.00956848 0.00412758 0.02043944mr_scatter_plot(d_mr,d)## $`prot-a-3024.ieu-b-4760`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 prot-a-3024 ieu-b-4760d <- make_dat("ieu-b-4760", "prot-a-3024")## Extracting data for 9 SNP(s) from 1 GWAS(s)## Finding proxies for 2 SNPs in outcome prot-a-3024## Extracting data for 2 SNP(s) from 1 GWAS(s)## Harmonising Number of children || id:ieu-b-4760 (ieu-b-4760) and Transmembrane protease serine 11D || id:prot-a-3024 (prot-a-3024)d_mr<-mr(d)## Analysing 'ieu-b-4760' on 'prot-a-3024'd_mr## id.exposure id.outcome outcome
## 1 ieu-b-4760 prot-a-3024 Transmembrane protease serine 11D || id:prot-a-3024
## 2 ieu-b-4760 prot-a-3024 Transmembrane protease serine 11D || id:prot-a-3024
## 3 ieu-b-4760 prot-a-3024 Transmembrane protease serine 11D || id:prot-a-3024
## 4 ieu-b-4760 prot-a-3024 Transmembrane protease serine 11D || id:prot-a-3024
## 5 ieu-b-4760 prot-a-3024 Transmembrane protease serine 11D || id:prot-a-3024
## exposure method nsnp
## 1 Number of children || id:ieu-b-4760 MR Egger 7
## 2 Number of children || id:ieu-b-4760 Weighted median 7
## 3 Number of children || id:ieu-b-4760 Inverse variance weighted 7
## 4 Number of children || id:ieu-b-4760 Simple mode 7
## 5 Number of children || id:ieu-b-4760 Weighted mode 7
## b se pval
## 1 -11.8320016 8.8674827 0.2396404
## 2 -0.3668881 0.8668234 0.6721085
## 3 1.6164493 1.7758092 0.3626850
## 4 -0.3934730 1.0574449 0.7226082
## 5 -0.4219379 0.9412930 0.6697026mr_scatter_plot(d_mr,d)## $`ieu-b-4760.prot-a-3024`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ieu-b-4760 prot-a-3024