Power calcuations for MR of RP expression on breast cancer in BCAC 2020

power

Charleen D. Adams1 and Bernardo Lemos1,2

1Department of Environmental Health, Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
2Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA

Abstract

Power calculation for MR of RP expression on BC in BCAC 2020.

Contents

mkdir /n/home04/cdadams/power
cd /n/home04/cdadams/power
git init 
echo "# Power calcuations for Aim 2

Power estimates were done for BCAC's 2020 overall GWAS of breast cancer, which has a sample size of 247173 (0.54% cases) and by using r2 values of 0.01 and 0.02. R2 refers to the proportion of the variance in RP expression explained by an eQTL or set of eQTLs in a meta-analysis. Values of 0.01 and 0.02 are common for epidemiological traits. However, since gene expression is a molecular phenotype and the SNPs chosen are within +/- 1 Mb of the transcription start of the genes, the proportion of variance explained is likely to be greater. Our calculations are very conservative. They show that we have >80% power to detect causal effects (odds ratios) of 0.85 (decreased risk) and 1.15 (increased risk) for both (0.01 and 0.02 r2 values).

The power calculations were perfomed using 'mRnd: Power calculations for Mendelian Randomization' (available at: https://shiny.cnsgenomics.com/mRnd/). 

Citation: Calculating statistical power in Mendelian randomization studies Marie-Jo A Brion, Konstantin Shakhbazov, Peter M Visscher International Journal of Epidemiology 2013 42: 1497-1501.

The repo contains:

- Data (power.csv)
- Png (power.png)
- Rmd (power.Rmd)
- Rpubs: https://rpubs.com/Charleen_D_Adams/755056

<hr style="border:2px solid blue"> </hr>
">> README.md

git add README.md
git commit -m "Power calcuations for Aim 2"
git branch -M main

git remote add origin https://github.com/LabLemos/power.git
git push -u origin main

# Add .Rmd
git add power.Rmd
git commit -m "Script"
git push --all

# Add power.png
git add power.png
git commit -m "png, dpi=300"
git push --all

# Add power.csv
git add  power.csv
git commit -m ""
git push --all

0.1 Power