GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies

被引：144

作者：

Gogarten, Stephanie M. ^{[1
]}

Bhangale, Tushar ^{[1
,2
]}

Conomos, Matthew P. ^{[1
]}

Laurie, Cecelia A. ^{[1
]}

McHugh, Caitlin P. ^{[1
]}

Painter, Ian ^{[3
]}

Zheng, Xiuwen ^{[1
]}

Crosslin, David R. ^{[1
]}

Levine, David ^{[1
]}

Lumley, Thomas ^{[1
,4
]}

Nelson, Sarah C. ^{[1
]}

Rice, Kenneth ^{[1
]}

Shen, Jess ^{[1
]}

Swarnkar, Rohit ^{[1
]}

Weir, Bruce S. ^{[1
]}

Laurie, Cathy C. ^{[1
]}

机构：

[1] Univ Washington, Dept Biostat, Seattle, WA 98195 USA

[2] Genentech Inc, Dept Bioinformat & Computat Biol, San Francisco, CA 94080 USA

[3] Univ Washington, Dept Hlth Serv, Seattle, WA 98195 USA

[4] Univ Auckland, Dept Stat, Auckland 1, New Zealand

来源：

BIOINFORMATICS | 2012年 / 28卷 / 24期

基金：

美国国家卫生研究院;

关键词：

MOSAICISM;

D O I：

10.1093/bioinformatics/bts610

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

SUMMARY: GWASTools is an R/Bioconductor package for quality control and analysis of genome-wide association studies (GWAS). GWASTools brings the interactive capability and extensive statistical libraries of R to GWAS. Data are stored in NetCDF format to accommodate extremely large datasets that cannot fit within R's memory limits. The documentation includes instructions for converting data from multiple formats, including variants called from sequencing. GWASTools provides a convenient interface for linking genotypes and intensity data with sample and single nucleotide polymorphism annotation. Availability and implementation: GWASTools is implemented in R and is available from Bioconductor (http://www.bioconductor.org). An extensive vignette detailing a recommended work flow is included.

引用

页码：3329 / 3331

页数：3

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