Increased genetic contribution to wellbeing during the COVID-19 pandemic

Quality control

Sample quality control is done in: ./scripts/sampleQc.R

PGS calculation

Polygenic scores (PGSs) are calculated using the scripts in ./scripts/pgs-calculations. The scripts are described here.

Combine and filter questionnaire data and recode answer options

The scripts used for combining and questionnaire data and recode the answer options can be found in ./scripts/combine-filter-and-recode-questionnaire-data. Description is available here

Relation PGSs and traits

Longitudinal models

The data was converted to long format and other preprocessing needed for the mixed models are done here: /scripts/prepareForLongitudinalModels.R

The longitudinal models are fitted by: /scripts/longitudinalModels.R

The plots of the longitudinal models are made using: /scripts/plotLongitudinalModels.R

Baseline associations and sensitivity analysis

The scripts used for the baseline associations are avaiable in the ./scripts/baseline-and-validation-models/ directory. Description can be found here

Correlation with nation-wide statistics

A number of publicly available data sources reflecting the development of the pandemic were selected for correlation with subjective quality of life. After preprocessing of the PGSs and traits, ./scripts/nationWideCorrelations.R is used for creating figures and correlations.

Correlating outcome variables and PGSs in baseline sample set

We correlated 5 outcome variables that were assumed to tag the same genetics * time effect. Additionally, we correlated polygenic scores for all PGSs in the baseline sample set. After preprocessing of the PGSs and traits, ./scripts/correlationsForBaselineSamples.R is used for creating figures and calculating these correlations.

Comparison of included samples and invited samples for polygenic scores

A comparison was done betwen samples that were invited in the studies and samples that were included for the polygenic scores. After preprocessing of the PGSs and traits, ./scripts/pgsParticipationComparison.R is used for creating figures and performing significance tests.

Visualizing distributions of questions

After preprocesssing of the PGSs and traits, ./scripts/plotOutcomeDistributions.R can be used to plot the distributions of each of the outcome variables for which we attempted to fit a time interaction.

Manuscript figures

• Fig2: ./scripts/plotHeatmapBaselineModels.R
• Fig3: ./scripts/qolPlot.R
• Fig4: ./scripts/c19Plot.R