BMI
Clare Horscroft
04/08/2021
Investigating BMI, weight, and fat 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 detailsBMI
d <- make_dat("ukb-b-19953", "ukb-b-2227")## API: public: http://gwas-api.mrcieu.ac.uk/## Extracting data for 458 SNP(s) from 1 GWAS(s)## Finding proxies for 1 SNPs in outcome ukb-b-2227## Extracting data for 1 SNP(s) from 1 GWAS(s)## Harmonising Body mass index (BMI) || id:ukb-b-19953 (ukb-b-19953) and Number of children fathered || id:ukb-b-2227 (ukb-b-2227)## Removing the following SNPs for incompatible alleles:
## rs7928320d_mr<-mr(d)## Analysing 'ukb-b-19953' on 'ukb-b-2227'd_mr## id.exposure id.outcome outcome
## 1 ukb-b-19953 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 2 ukb-b-19953 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 3 ukb-b-19953 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 4 ukb-b-19953 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 5 ukb-b-19953 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## exposure method nsnp
## 1 Body mass index (BMI) || id:ukb-b-19953 MR Egger 457
## 2 Body mass index (BMI) || id:ukb-b-19953 Weighted median 457
## 3 Body mass index (BMI) || id:ukb-b-19953 Inverse variance weighted 457
## 4 Body mass index (BMI) || id:ukb-b-19953 Simple mode 457
## 5 Body mass index (BMI) || id:ukb-b-19953 Weighted mode 457
## b se pval
## 1 -0.004581618 0.024882688 8.539945e-01
## 2 0.055098582 0.013844170 6.894073e-05
## 3 0.061133500 0.009222218 3.381132e-11
## 4 0.045424774 0.048023688 3.447094e-01
## 5 0.026829392 0.026654079 3.146718e-01mr_scatter_plot(d_mr,d)## $`ukb-b-19953.ukb-b-2227`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-19953 ukb-b-2227d <- make_dat("ukb-b-2227", "ukb-b-19953")## Extracting data for 3 SNP(s) from 1 GWAS(s)## Harmonising Number of children fathered || id:ukb-b-2227 (ukb-b-2227) and Body mass index (BMI) || id:ukb-b-19953 (ukb-b-19953)d_mr<-mr(d)## Analysing 'ukb-b-2227' on 'ukb-b-19953'd_mr## id.exposure id.outcome outcome
## 1 ukb-b-2227 ukb-b-19953 Body mass index (BMI) || id:ukb-b-19953
## 2 ukb-b-2227 ukb-b-19953 Body mass index (BMI) || id:ukb-b-19953
## 3 ukb-b-2227 ukb-b-19953 Body mass index (BMI) || id:ukb-b-19953
## 4 ukb-b-2227 ukb-b-19953 Body mass index (BMI) || id:ukb-b-19953
## 5 ukb-b-2227 ukb-b-19953 Body mass index (BMI) || id:ukb-b-19953
## 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 5.951723150 3.9084715 0.3699193
## 2 0.085717621 0.1131351 0.4486562
## 3 0.295145325 0.2772422 0.2870680
## 4 -0.034403342 0.1189824 0.7996865
## 5 0.002781542 0.1183355 0.9833814mr_scatter_plot(d_mr,d)## $`ukb-b-2227.ukb-b-19953`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-2227 ukb-b-19953BMI highly related with number of children, no evidence of reverse causality (i.e. more children does not cause higher BMI)
Weight
d <- make_dat("ukb-b-11842", "ukb-b-2227")## Extracting data for 498 SNP(s) from 1 GWAS(s)## Harmonising Weight || id:ukb-b-11842 (ukb-b-11842) and Number of children fathered || id:ukb-b-2227 (ukb-b-2227)d_mr<-mr(d)## Analysing 'ukb-b-11842' on 'ukb-b-2227'd_mr## id.exposure id.outcome outcome
## 1 ukb-b-11842 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 2 ukb-b-11842 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 3 ukb-b-11842 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 4 ukb-b-11842 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 5 ukb-b-11842 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## exposure method nsnp b
## 1 Weight || id:ukb-b-11842 MR Egger 498 -0.02426350
## 2 Weight || id:ukb-b-11842 Weighted median 498 0.05723154
## 3 Weight || id:ukb-b-11842 Inverse variance weighted 498 0.06280052
## 4 Weight || id:ukb-b-11842 Simple mode 498 0.07846674
## 5 Weight || id:ukb-b-11842 Weighted mode 498 0.04941912
## se pval
## 1 0.023908980 3.106827e-01
## 2 0.013456353 2.108083e-05
## 3 0.009526746 4.338772e-11
## 4 0.043957770 7.486326e-02
## 5 0.027114181 6.896017e-02mr_scatter_plot(d_mr,d)## $`ukb-b-11842.ukb-b-2227`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-11842 ukb-b-2227d <- make_dat("ukb-b-2227", "ukb-b-11842")## Extracting data for 3 SNP(s) from 1 GWAS(s)## Harmonising Number of children fathered || id:ukb-b-2227 (ukb-b-2227) and Weight || id:ukb-b-11842 (ukb-b-11842)d_mr<-mr(d)## Analysing 'ukb-b-2227' on 'ukb-b-11842'd_mr## id.exposure id.outcome outcome
## 1 ukb-b-2227 ukb-b-11842 Weight || id:ukb-b-11842
## 2 ukb-b-2227 ukb-b-11842 Weight || id:ukb-b-11842
## 3 ukb-b-2227 ukb-b-11842 Weight || id:ukb-b-11842
## 4 ukb-b-2227 ukb-b-11842 Weight || id:ukb-b-11842
## 5 ukb-b-2227 ukb-b-11842 Weight || id:ukb-b-11842
## 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 6.15708927 3.2320759 0.3077398
## 2 0.13066290 0.1083773 0.2279603
## 3 0.29134377 0.2700865 0.2807192
## 4 0.03290606 0.1326531 0.8272320
## 5 0.07993650 0.1204604 0.5752098mr_scatter_plot(d_mr,d)## $`ukb-b-2227.ukb-b-11842`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-2227 ukb-b-11842d <- mv_extract_exposures(c("ukb-b-11842", "ukb-b-19953"))## Please look at vignettes for options on running this locally if you need to run many instances of this command.## Clumping 1, 874 variants, using EUR population reference## Removing 383 of 874 variants due to LD with other variants or absence from LD reference panel## Extracting data for 491 SNP(s) from 2 GWAS(s)## Harmonising Weight || id:ukb-b-11842 (ukb-b-11842) and Body mass index (BMI) || id:ukb-b-19953 (ukb-b-19953)## Removing the following SNPs for being palindromic with intermediate allele frequencies:
## rs11250094, rs12507026, rs13264909, rs1454687, rs1860750, rs2396625, rs3097851, rs59086897, rs6597975, rs7568228, rs7942152, rs9614090o <- extract_outcome_data(d$SNP, "ukb-b-2227")## Extracting data for 491 SNP(s) from 1 GWAS(s)d <- mv_harmonise_data(d, o)## Harmonising Weight || id:ukb-b-11842 (ukb-b-11842) and Number of children fathered || id:ukb-b-2227 (ukb-b-2227)
## Removing the following SNPs for being palindromic with intermediate allele frequencies:
## rs11250094, rs12507026, rs13264909, rs1454687, rs1860750, rs2396625, rs3097851, rs59086897, rs6597975, rs7568228, rs7942152, rs9614090mv_multiple(d)## $result
## id.exposure exposure id.outcome
## 1 ukb-b-11842 Weight || id:ukb-b-11842 ukb-b-2227
## 2 ukb-b-19953 Body mass index (BMI) || id:ukb-b-19953 ukb-b-2227
## outcome nsnp b se
## 1 Number of children fathered || id:ukb-b-2227 411 0.03221459 0.02104255
## 2 Number of children fathered || id:ukb-b-2227 321 0.03932456 0.02126834
## pval
## 1 0.12578770
## 2 0.06446189Weight effect explained by BMI.
Waist circumference
d <- make_dat("ukb-b-9405", "ukb-b-2227")## Extracting data for 374 SNP(s) from 1 GWAS(s)## Harmonising Waist circumference || id:ukb-b-9405 (ukb-b-9405) and Number of children fathered || id:ukb-b-2227 (ukb-b-2227)## Removing the following SNPs for incompatible alleles:
## rs156902d_mr<-mr(d)## Analysing 'ukb-b-9405' on 'ukb-b-2227'd_mr## id.exposure id.outcome outcome
## 1 ukb-b-9405 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 2 ukb-b-9405 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 3 ukb-b-9405 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 4 ukb-b-9405 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 5 ukb-b-9405 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## exposure method nsnp
## 1 Waist circumference || id:ukb-b-9405 MR Egger 374
## 2 Waist circumference || id:ukb-b-9405 Weighted median 374
## 3 Waist circumference || id:ukb-b-9405 Inverse variance weighted 374
## 4 Waist circumference || id:ukb-b-9405 Simple mode 374
## 5 Waist circumference || id:ukb-b-9405 Weighted mode 374
## b se pval
## 1 0.008023028 0.03425800 8.149630e-01
## 2 0.064436516 0.01721821 1.823093e-04
## 3 0.064224124 0.01195098 7.702536e-08
## 4 0.108341081 0.06015759 7.251764e-02
## 5 0.069433598 0.03447275 4.471030e-02mr_scatter_plot(d_mr,d)## $`ukb-b-9405.ukb-b-2227`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-9405 ukb-b-2227d <- make_dat("ukb-b-2227", "ukb-b-9405")## Extracting data for 3 SNP(s) from 1 GWAS(s)## Harmonising Number of children fathered || id:ukb-b-2227 (ukb-b-2227) and Waist circumference || id:ukb-b-9405 (ukb-b-9405)d_mr<-mr(d)## Analysing 'ukb-b-2227' on 'ukb-b-9405'd_mr## id.exposure id.outcome outcome
## 1 ukb-b-2227 ukb-b-9405 Waist circumference || id:ukb-b-9405
## 2 ukb-b-2227 ukb-b-9405 Waist circumference || id:ukb-b-9405
## 3 ukb-b-2227 ukb-b-9405 Waist circumference || id:ukb-b-9405
## 4 ukb-b-2227 ukb-b-9405 Waist circumference || id:ukb-b-9405
## 5 ukb-b-2227 ukb-b-9405 Waist circumference || id:ukb-b-9405
## 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 3.99466625 3.22446472 0.4323357
## 2 0.00986069 0.09382822 0.9163020
## 3 0.13968488 0.20265295 0.4906463
## 4 -0.11166098 0.09753967 0.3708232
## 5 -0.09387958 0.09898322 0.4430128mr_scatter_plot(d_mr,d)## $`ukb-b-2227.ukb-b-9405`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-2227 ukb-b-9405Body fat
Whole body fat mass
d <- make_dat("ukb-b-19393", "ukb-b-2227")## Extracting data for 435 SNP(s) from 1 GWAS(s)## Harmonising Whole body fat mass || id:ukb-b-19393 (ukb-b-19393) and Number of children fathered || id:ukb-b-2227 (ukb-b-2227)## Removing the following SNPs for incompatible alleles:
## rs2731238, rs2943634d_mr<-mr(d)## Analysing 'ukb-b-19393' on 'ukb-b-2227'd_mr## id.exposure id.outcome outcome
## 1 ukb-b-19393 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 2 ukb-b-19393 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 3 ukb-b-19393 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 4 ukb-b-19393 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 5 ukb-b-19393 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## exposure method nsnp
## 1 Whole body fat mass || id:ukb-b-19393 MR Egger 435
## 2 Whole body fat mass || id:ukb-b-19393 Weighted median 435
## 3 Whole body fat mass || id:ukb-b-19393 Inverse variance weighted 435
## 4 Whole body fat mass || id:ukb-b-19393 Simple mode 435
## 5 Whole body fat mass || id:ukb-b-19393 Weighted mode 435
## b se pval
## 1 -0.02884213 0.027163866 2.889261e-01
## 2 0.03257871 0.013622263 1.677610e-02
## 3 0.04998433 0.009738173 2.854257e-07
## 4 0.03521918 0.047108864 4.550987e-01
## 5 0.02254806 0.030071127 4.537668e-01mr_scatter_plot(d_mr,d)## $`ukb-b-19393.ukb-b-2227`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-19393 ukb-b-2227d <- make_dat("ukb-b-2227", "ukb-b-19393")## Extracting data for 3 SNP(s) from 1 GWAS(s)## Harmonising Number of children fathered || id:ukb-b-2227 (ukb-b-2227) and Whole body fat mass || id:ukb-b-19393 (ukb-b-19393)d_mr<-mr(d)## Analysing 'ukb-b-2227' on 'ukb-b-19393'd_mr## id.exposure id.outcome outcome
## 1 ukb-b-2227 ukb-b-19393 Whole body fat mass || id:ukb-b-19393
## 2 ukb-b-2227 ukb-b-19393 Whole body fat mass || id:ukb-b-19393
## 3 ukb-b-2227 ukb-b-19393 Whole body fat mass || id:ukb-b-19393
## 4 ukb-b-2227 ukb-b-19393 Whole body fat mass || id:ukb-b-19393
## 5 ukb-b-2227 ukb-b-19393 Whole body fat mass || id:ukb-b-19393
## 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 4.893924482 2.8966624 0.3402316
## 2 0.113363682 0.1107168 0.3058794
## 3 0.222547662 0.2216849 0.3154308
## 4 -0.007752152 0.1466089 0.9626368
## 5 0.035163921 0.1416567 0.8271156mr_scatter_plot(d_mr,d)## $`ukb-b-2227.ukb-b-19393`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-2227 ukb-b-19393Impedance of whole body
d <- make_dat("ukb-b-19921", "ukb-b-2227")## Extracting data for 528 SNP(s) from 1 GWAS(s)## Harmonising Impedance of whole body || id:ukb-b-19921 (ukb-b-19921) and Number of children fathered || id:ukb-b-2227 (ukb-b-2227)d_mr<-mr(d)## Analysing 'ukb-b-19921' on 'ukb-b-2227'd_mr## id.exposure id.outcome outcome
## 1 ukb-b-19921 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 2 ukb-b-19921 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 3 ukb-b-19921 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 4 ukb-b-19921 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 5 ukb-b-19921 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## exposure method nsnp
## 1 Impedance of whole body || id:ukb-b-19921 MR Egger 528
## 2 Impedance of whole body || id:ukb-b-19921 Weighted median 528
## 3 Impedance of whole body || id:ukb-b-19921 Inverse variance weighted 528
## 4 Impedance of whole body || id:ukb-b-19921 Simple mode 528
## 5 Impedance of whole body || id:ukb-b-19921 Weighted mode 528
## b se pval
## 1 -0.06383621 0.02793744 2.271181e-02
## 2 -0.05126154 0.01448876 4.031385e-04
## 3 -0.06250341 0.01052276 2.853210e-09
## 4 -0.03050755 0.05021212 5.437322e-01
## 5 -0.03539376 0.03258163 2.778383e-01mr_scatter_plot(d_mr,d)## $`ukb-b-19921.ukb-b-2227`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-19921 ukb-b-2227d <- make_dat("ukb-b-2227", "ukb-b-19921")## Extracting data for 3 SNP(s) from 1 GWAS(s)## Harmonising Number of children fathered || id:ukb-b-2227 (ukb-b-2227) and Impedance of whole body || id:ukb-b-19921 (ukb-b-19921)d_mr<-mr(d)## Analysing 'ukb-b-2227' on 'ukb-b-19921'd_mr## id.exposure id.outcome outcome
## 1 ukb-b-2227 ukb-b-19921 Impedance of whole body || id:ukb-b-19921
## 2 ukb-b-2227 ukb-b-19921 Impedance of whole body || id:ukb-b-19921
## 3 ukb-b-2227 ukb-b-19921 Impedance of whole body || id:ukb-b-19921
## 4 ukb-b-2227 ukb-b-19921 Impedance of whole body || id:ukb-b-19921
## 5 ukb-b-2227 ukb-b-19921 Impedance of whole body || id:ukb-b-19921
## 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 -6.007655685 4.26370472 0.3929308
## 2 -0.055783139 0.08221893 0.4974733
## 3 -0.319078507 0.28662457 0.2656105
## 4 0.036726316 0.08267025 0.7003063
## 5 0.002044616 0.08084748 0.9821203mr_scatter_plot(d_mr,d)## $`ukb-b-2227.ukb-b-19921`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-2227 ukb-b-19921Appendicular lean mass
d <- make_dat("ebi-a-GCST90000025", "ukb-b-2227")## Extracting data for 690 SNP(s) from 1 GWAS(s)## Finding proxies for 117 SNPs in outcome ukb-b-2227## Extracting data for 117 SNP(s) from 1 GWAS(s)## Harmonising Appendicular lean mass || id:ebi-a-GCST90000025 (ebi-a-GCST90000025) and Number of children fathered || id:ukb-b-2227 (ukb-b-2227)## Removing the following SNPs for incompatible alleles:
## rs664317, rs7543202, rs9640283d_mr<-mr(d)## Analysing 'ebi-a-GCST90000025' on 'ukb-b-2227'd_mr## id.exposure id.outcome outcome
## 1 ebi-a-GCST90000025 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 2 ebi-a-GCST90000025 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 3 ebi-a-GCST90000025 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 4 ebi-a-GCST90000025 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 5 ebi-a-GCST90000025 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## exposure method
## 1 Appendicular lean mass || id:ebi-a-GCST90000025 MR Egger
## 2 Appendicular lean mass || id:ebi-a-GCST90000025 Weighted median
## 3 Appendicular lean mass || id:ebi-a-GCST90000025 Inverse variance weighted
## 4 Appendicular lean mass || id:ebi-a-GCST90000025 Simple mode
## 5 Appendicular lean mass || id:ebi-a-GCST90000025 Weighted mode
## nsnp b se pval
## 1 622 0.02806694 0.014367233 5.120521e-02
## 2 622 0.03705166 0.008786322 2.476062e-05
## 3 622 0.01670773 0.006184126 6.898351e-03
## 4 622 0.05729864 0.028053127 4.152329e-02
## 5 622 0.05272846 0.019612598 7.369979e-03mr_scatter_plot(d_mr,d)## $`ebi-a-GCST90000025.ukb-b-2227`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ebi-a-GCST90000025 ukb-b-2227d <- make_dat("ukb-b-2227", "ebi-a-GCST90000025")## Extracting data for 3 SNP(s) from 1 GWAS(s)## Harmonising Number of children fathered || id:ukb-b-2227 (ukb-b-2227) and Appendicular lean mass || id:ebi-a-GCST90000025 (ebi-a-GCST90000025)d_mr<-mr(d)## Analysing 'ukb-b-2227' on 'ebi-a-GCST90000025'd_mr## id.exposure id.outcome
## 1 ukb-b-2227 ebi-a-GCST90000025
## 2 ukb-b-2227 ebi-a-GCST90000025
## 3 ukb-b-2227 ebi-a-GCST90000025
## 4 ukb-b-2227 ebi-a-GCST90000025
## 5 ukb-b-2227 ebi-a-GCST90000025
## outcome
## 1 Appendicular lean mass || id:ebi-a-GCST90000025
## 2 Appendicular lean mass || id:ebi-a-GCST90000025
## 3 Appendicular lean mass || id:ebi-a-GCST90000025
## 4 Appendicular lean mass || id:ebi-a-GCST90000025
## 5 Appendicular lean mass || id:ebi-a-GCST90000025
## 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 4.4690983 2.1298815 0.28312801
## 2 0.1957767 0.1068304 0.06686314
## 3 0.2796714 0.1920725 0.14537257
## 4 0.1070283 0.1722546 0.59775834
## 5 0.1402050 0.1666289 0.48868356mr_scatter_plot(d_mr,d)## $`ukb-b-2227.ebi-a-GCST90000025`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-2227 ebi-a-GCST90000025Basal metabolic rate
d <- make_dat("ukb-b-16446", "ukb-b-2227")## Warning in .fun(piece, ...): Duplicated SNPs present in exposure data for phenotype 'Basal metabolic rate || id:ukb-b-16446. Just keeping the first instance:
## rs3129962## Extracting data for 546 SNP(s) from 1 GWAS(s)## Finding proxies for 1 SNPs in outcome ukb-b-2227## Extracting data for 1 SNP(s) from 1 GWAS(s)## Server code: 502; Server is possibly experiencing traffic, trying again...## Retry succeeded!## Harmonising Basal metabolic rate || id:ukb-b-16446 (ukb-b-16446) and Number of children fathered || id:ukb-b-2227 (ukb-b-2227)## Removing the following SNPs for incompatible alleles:
## rs3129962d_mr<-mr(d)## Analysing 'ukb-b-16446' on 'ukb-b-2227'd_mr## id.exposure id.outcome outcome
## 1 ukb-b-16446 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 2 ukb-b-16446 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 3 ukb-b-16446 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 4 ukb-b-16446 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## 5 ukb-b-16446 ukb-b-2227 Number of children fathered || id:ukb-b-2227
## exposure method nsnp
## 1 Basal metabolic rate || id:ukb-b-16446 MR Egger 545
## 2 Basal metabolic rate || id:ukb-b-16446 Weighted median 545
## 3 Basal metabolic rate || id:ukb-b-16446 Inverse variance weighted 545
## 4 Basal metabolic rate || id:ukb-b-16446 Simple mode 545
## 5 Basal metabolic rate || id:ukb-b-16446 Weighted mode 545
## b se pval
## 1 0.009200946 0.02661346 7.296831e-01
## 2 0.056846118 0.01572067 2.991779e-04
## 3 0.050274266 0.01107546 5.645454e-06
## 4 0.099284964 0.05065919 5.052218e-02
## 5 0.080129286 0.03345706 1.695809e-02mr_scatter_plot(d_mr,d)## $`ukb-b-16446.ukb-b-2227`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-16446 ukb-b-2227d <- make_dat("ukb-b-2227", "ukb-b-16446")## Extracting data for 3 SNP(s) from 1 GWAS(s)## Harmonising Number of children fathered || id:ukb-b-2227 (ukb-b-2227) and Basal metabolic rate || id:ukb-b-16446 (ukb-b-16446)d_mr<-mr(d)## Analysing 'ukb-b-2227' on 'ukb-b-16446'd_mr## id.exposure id.outcome outcome
## 1 ukb-b-2227 ukb-b-16446 Basal metabolic rate || id:ukb-b-16446
## 2 ukb-b-2227 ukb-b-16446 Basal metabolic rate || id:ukb-b-16446
## 3 ukb-b-2227 ukb-b-16446 Basal metabolic rate || id:ukb-b-16446
## 4 ukb-b-2227 ukb-b-16446 Basal metabolic rate || id:ukb-b-16446
## 5 ukb-b-2227 ukb-b-16446 Basal metabolic rate || id:ukb-b-16446
## 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 5.28653610 2.95870279 0.3248258
## 2 0.09624344 0.07661607 0.2090514
## 3 0.26702906 0.23494310 0.2557185
## 4 0.03087537 0.09808337 0.7827293
## 5 0.05120012 0.09201777 0.6338736mr_scatter_plot(d_mr,d)## $`ukb-b-2227.ukb-b-16446`
##
## attr(,"split_type")
## [1] "data.frame"
## attr(,"split_labels")
## id.exposure id.outcome
## 1 ukb-b-2227 ukb-b-16446d <- mv_extract_exposures(c("ukb-b-16446", "ukb-b-19953"))## Warning in .fun(piece, ...): Duplicated SNPs present in exposure data for phenotype 'Basal metabolic rate || id:ukb-b-16446. Just keeping the first instance:
## rs3129962## Please look at vignettes for options on running this locally if you need to run many instances of this command.## Clumping 1, 965 variants, using EUR population reference## Removing 412 of 965 variants due to LD with other variants or absence from LD reference panel## Extracting data for 553 SNP(s) from 2 GWAS(s)## Warning in .fun(piece, ...): Duplicated SNPs present in exposure data for phenotype 'Basal metabolic rate || id:ukb-b-16446. Just keeping the first instance:
## rs3740591## Harmonising Basal metabolic rate || id:ukb-b-16446 (ukb-b-16446) and Body mass index (BMI) || id:ukb-b-19953 (ukb-b-19953)## Removing the following SNPs for incompatible alleles:
## rs3740591## Removing the following SNPs for being palindromic with intermediate allele frequencies:
## rs10883560, rs11250094, rs11664336, rs12507026, rs1316312, rs13264909, rs1454687, rs165656, rs2396625, rs3740591, rs3771382, rs37964, rs4255484, rs59086897, rs6597975, rs9882731, rs9976812o <- extract_outcome_data(d$SNP, "ukb-b-2227")## Extracting data for 552 SNP(s) from 1 GWAS(s)d <- mv_harmonise_data(d, o)## Harmonising Basal metabolic rate || id:ukb-b-16446 (ukb-b-16446) and Number of children fathered || id:ukb-b-2227 (ukb-b-2227)## Removing the following SNPs for being palindromic with intermediate allele frequencies:
## rs10883560, rs11250094, rs11664336, rs12507026, rs1316312, rs13264909, rs1454687, rs165656, rs2396625, rs3771382, rs37964, rs4255484, rs59086897, rs6597975, rs9882731, rs9976812mv_multiple(d)## $result
## id.exposure exposure id.outcome
## 1 ukb-b-16446 Basal metabolic rate || id:ukb-b-16446 ukb-b-2227
## 2 ukb-b-19953 Body mass index (BMI) || id:ukb-b-19953 ukb-b-2227
## outcome nsnp b se
## 1 Number of children fathered || id:ukb-b-2227 446 0.02679504 0.01572631
## 2 Number of children fathered || id:ukb-b-2227 234 0.03778874 0.01457291
## pval
## 1 0.088411827
## 2 0.009512033