powerEQTL: an R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis.
powerEQTL: an R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis.
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DOI：
10.1093/bioinformatics/btab385
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发表时间：
2021-11-18
期刊：
影响因子：
5.8
通讯作者：
Qiu, Weiliang
中科院分区：
文献类型：
--
作者：
Dong, Xianjun;Li, Xiaoqi;Chang, Tzuu-Wang;Scherzer, Clemens R.;Weiss, Scott T.;Qiu, Weiliang
全基因组关联研究（GWAS）已经揭示了常见疾病的数千个遗传位点。后GWAS时代的主要挑战之一是了解遗传变异的因果关系。表达数量性状基因座（eQTL）分析是解决这一问题的有效方法，它通过在一个有足够把握的队列中检测基因表达和遗传变异之间的关系。然而，确定将检测到具有特定等位基因频率的变体以足够功效与基因表达相关联的样本量常常是一个挑战。这对于单细胞RNAseq研究来说是一项特别困难的任务。因此，需要一种用户友好的工具来估计eQTL分析在散装组织和单细胞数据中的统计功效。在这里，我们提出了一个R软件包称为powerEQTL与灵活的功能来估计功率，最小样本大小或可检测的次要等位基因频率的散装组织和单细胞eQTL分析。还提供了一个用户友好的、无程序的网络应用程序，允许用户以交互方式计算和可视化参数。powerEQTLR包的源代码和在线教程可以在CRAN：https://cran.r-project.org/web/packages/powerEQTL/上免费获得。R shiny应用程序在https://bwhbioinfo.shinyapps.io/powerEQTL/上公开托管。 补充数据可在Bioinformatics在线获得。
Genome-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 is 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 frequently a challenge 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 a particularly difficult task for single-cell RNAseq studies. Therefore, a user-friendly tool to estimate statistical power for eQTL analyses in both bulk tissue and single-cell data is needed. Here, we presented an R package called powerEQTL with flexible functions to estimate power, minimal sample size or detectable minor allele frequency for both bulk tissue and single-cell eQTL analysis. A user-friendly, program-free web application is also provided, allowing users to calculate and visualize the parameters interactively. The 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/. Supplementary data are available at Bioinformatics online.
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影响因子：
30.8
作者：
eGTEx Project
通讯作者：
eGTEx Project
影响因子：
14.9
作者：
Buniello, Annalisa;MacArthur, Jacqueline A. L.;Parkinson, Helen
通讯作者：
Parkinson, Helen
影响因子：
4.6
作者：
Zhang, Zeyu;Yu, Danyang;Qiu, Weiliang
通讯作者：
Qiu, Weiliang
DOI：
10.1126/science.1262110
发表时间：
2015-05-08
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
GTEx Consortium
通讯作者：
GTEx Consortium
影响因子：
16.6
作者：
Cuomo, Anna S. E.;Seaton, Daniel D.;Stegle, Oliver
通讯作者：
Stegle, Oliver