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bioRxiv · 10.1101/2020.12.15.422954

powerEQTL: An R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis

Dong, X.·Li, X.·Chang, T.-W.·Weiss, S. T.·Qiu, W.
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Abstract

SummaryGenome-wide association studies (GWAS) have revealed thousands of genetic loci for common diseases. One of the main challenges in the post-GWAS era is to understand the causality of the genetic variants. Expression quantitative trait locus (eQTL) analysis has been proven to be an effective way to address this question by examining the relationship between gene expression and genetic variation in a sufficiently powered cohort. However, it is often tricky to determine the sample size at which a variant with a specific allele frequency will be detected to associate with gene expression with sufficient power. This is particularly demanding with single-cell RNAseq studies. Therefore, a user-friendly tool to perform power analysis for eQTL at both bulk tissue and single-cell level will be critical. Here, we presented an R package called powerEQTL with flexible functions to calculate power, minimal sample size, or detectable minor allele frequency in both bulk tissue and single-cell eQTL analysis. A user-friendly, program-free web application is also provided, allowing customers to calculate and visualize the parameters interactively. Availability and implementationThe powerEQTL R package source code and online tutorial are freely available at CRAN: https://cran.r-project.org/web/packages/powerEQTL/. The R shiny application is publicly hosted at https://bwhbioinfo.shinyapps.io/powerEQTL/. ContactXianjun Dong (xdong@rics.bwh.harvard.edu), Weiliang Qiu (weiliang.qiu@sanofi.com) Supplementary informationSupplementary data are available at Bioinformatics online.

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Dong, X., Li, X., Chang, T.-W., Weiss, S. T., Qiu, W.. 2020-12-16. powerEQTL: An R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis. https://doi.org/10.1101/2020.12.15.422954

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