Last updated: 2021-09-15

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File Version Author Date Message
Rmd 7fd5143 Jenny Sjaarda 2021-09-15 add geographical impact Rmd
Rmd e7c62ad jennysjaarda 2021-09-15 adding Rmd of geographical impact

1 Background

  • Geographical location is clearly a strong indicator of couple choice.
  • Not only do couples tend to choose partners that are phenotypically similar to them (because of common interests, political views, etc.), but also because of location (i.e. convenience).
  • Geographical similarity induces genetic and in turn phenotypic similarity.
  • We sought to explore the impact of genography on mate-choice by adding PCs to the pipeline.

2 Analysis

2.1 GWAS of PCs

  • Performed GWAS of first 40 PCs, run using bgenie.
  • Sample selection: genetic, consenting, European sample (N = 408899), in attempt to best replicate the GWAS used in other analyses from the Neale lab.
  • Data transformation:
    • First, inverse normal rank tansformation (INT) was applied within the selected (this was done before dividing into sex-specific subgroups).
    • Next, PCs were residualized for age and sex.
  • GWAS was run in:
    • Entire sample (residualized for both age and sex).
    • Sex-specific subgroups (residualized for only age).
  • GWAS was not adjusted for PCs (as is typical in GWAS) because PCs are linearly independent of each other (although the sample used for PC calculation - by the UKB investigators - would be slightly different that our GWAS sample, so the PCs would not necessarily be completely linearly independent in this sample).

2.2 Correlation of PCs between couples

  • Test raw "phenotypic" correlation of PCs between partners in UKB.
  • As above, PCs were transformed using INT within genetic, consenting, European sample (N = 408899) and correlations were calculated within couples on the transformed PCs.

sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

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