综合变异基因基因频率分析管道和R包:easyVAF
Junxiao Hu1,2, Vida Alami1, Yonghua Zhuang1,2
1Biostatistics Shared Resource (RRID: SCR_021981), University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.
Molecular carcinogenesis
|August 22, 2023
概括
简单的VAF是一个新的R包,用于在不同组中比较变异性等位基因频率 (VAF),以确定与癌症相关的遗传变化. 它提供统计测试来分析VAF,帮助癌症研究和治疗反应评估.
科学领域:
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
- 癌症研究 癌症研究
背景情况:
- 身体序列变异对于癌症诊断,预后和治疗反应至关重要.
- 变异异基因频率 (VAF) 量化了突变率,反映了瘤克隆演变.
- 现有的工具缺乏跨群体的全面VAF比较功能.
研究的目的:
- 开发一个R包,easyVAF,用于在组内和组之间比较VAF.
- 提供统计测试,用于识别显著的遗传位置.
- 为VAF分析提供一个交互式R Shiny应用程序.
主要方法:
- 开发了R包的 easyVAF.
- 包括参数和非参数统计测试用于VAF比较.
- 使用模拟场景进行评估,并与现有测试进行比较.
主要成果:
- easyVAF为VAF分析提供了一个管道,从质量检查到组比较.
- 该包提供了三个统计测试,以平衡功率和I型错误率.
- 对于稀疏的数据,建议使用β-双项概率比率测试.
结论:
- 通过VAF比较,easyVAF促进了关键遗传位置的识别.
- 选择适当的统计测试对于准确的VAF分析至关重要.
- 该包及其应用程序增强了癌症研究中的VAF分析.
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