Last updated: 2021-09-14
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Knit directory: proxyMR/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 0365f37 | jennysjaarda | 2021-09-14 | add phenotype and couple selection schematic links |
| html | 7f198c6 | Jenny Sjaarda | 2021-09-14 | Build site. |
| Rmd | e3f688e | Jenny Sjaarda | 2021-09-14 | update some docs |
| Rmd | f8ee7b4 | jennysjaarda | 2021-09-14 | add a few Rmd notebooks |
Couples were defined and selected according to the following scheme
An overview of couple selection and exclusions can be seen here.
The initial UKBB sample comprised of N = 502616 individuals.
Each phenotype in the SGG database was filtered for the following criteria based on the genetic qc file (located here: /data/sgg2/jenny/data/UKBB_raw/geno/ukb_sqc_v2.txt):
excess.relatives=0putative.sex.chromosome.aneuploidy=0in.white.british.ancestry.subset==1Redacted samples and participants that removed consent were also excluded. Specifically, redacted samples are any IDs in c(-1, -2, -3), from the same genetic QC sample and the samples which removed consent, according to the exclusion file w16389_20200204.csv.
After filtering, N = 408899 individuals remained.
A few notes on the PHESANT processing:
PHESANT pipeline.Within the European, genetic, consenting sample, we limited to only individuals which came from households with exactly two participants in the UKBB based on the file: /data/sgg2/jenny/data/UKBB_raw/pheno/ukb6881.csv.
After filtering, N = 160694 individuals and N = 80347 couples remained.
Unrelated, household pairs were filtered to only include heterosexual couples.
After removing homosexual pairs, N = 158260 individuals and N = 79130 couples remained.
Finally, using the data at data-field 6141, "How are people in household related to participant", the heterosexual, unrelated, household pairs were filtered to only include couples who both responded Husband, wife, or partner.
After removing non-romantic pairs, N = 150062 individuals and N = 75031 couples remained.
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /data/sgg2/jenny/bin/R-4.1.0/lib64/R/lib/libRblas.so
LAPACK: /data/sgg2/jenny/bin/R-4.1.0/lib64/R/lib/libRlapack.so
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[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
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