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PreMeta: a tool to facilitate meta-analysis of rare-variant associations
BACKGROUND: Meta-analysis is essential to the discovery of rare variants that influence complex diseases and traits. Four major software packages, namely MASS, MetaSKAT, RAREMETAL, and seqMeta, have been developed to perform meta-analysis of rare-variant associations. These packages first generate s...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5310051/ https://www.ncbi.nlm.nih.gov/pubmed/28196472 http://dx.doi.org/10.1186/s12864-017-3573-1 |
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author | Tang, Zheng-Zheng Bunn, Paul Tao, Ran Liu, Zhouwen Lin, Dan-Yu |
author_facet | Tang, Zheng-Zheng Bunn, Paul Tao, Ran Liu, Zhouwen Lin, Dan-Yu |
author_sort | Tang, Zheng-Zheng |
collection | PubMed |
description | BACKGROUND: Meta-analysis is essential to the discovery of rare variants that influence complex diseases and traits. Four major software packages, namely MASS, MetaSKAT, RAREMETAL, and seqMeta, have been developed to perform meta-analysis of rare-variant associations. These packages first generate summary statistics for each study and then perform the meta-analysis by combining the summary statistics. Because of incompatible file formats and non-equivalent summary statistics, the output files from the study-level analysis of one package cannot be directly used to perform meta-analysis in another package. RESULTS: We developed a computationally efficient software program, PreMeta, to resolve the non-compatibility of the four software packages and to facilitate meta-analysis of large-scale sequencing studies in a consortium setting. PreMeta reformats the output files of study-level summary statistics generated by the four packages (text files produced by MASS and RAREMETAL, binary files produced by MetaSKAT, and R data files produced by seqMeta) and translates the summary statistics from one form to another, such that the summary statistics from any package can be used to perform meta-analysis in any other package. With this tool, consortium members are not required to use the same software for study-level analyses. In addition, PreMeta checks for allele mismatches, corrects summary statistics, and allows the rescaled inverse normal transformation to be performed at the meta-analysis stage by rescaling summary statistics. CONCLUSIONS: PreMeta processes summary statistics from the four packages to make them compatible and avoids the need to redo study-level analyses. PreMeta documentation and executable are available at: http://dlin.web.unc.edu/software/premeta. |
format | Online Article Text |
id | pubmed-5310051 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-53100512017-03-13 PreMeta: a tool to facilitate meta-analysis of rare-variant associations Tang, Zheng-Zheng Bunn, Paul Tao, Ran Liu, Zhouwen Lin, Dan-Yu BMC Genomics Software BACKGROUND: Meta-analysis is essential to the discovery of rare variants that influence complex diseases and traits. Four major software packages, namely MASS, MetaSKAT, RAREMETAL, and seqMeta, have been developed to perform meta-analysis of rare-variant associations. These packages first generate summary statistics for each study and then perform the meta-analysis by combining the summary statistics. Because of incompatible file formats and non-equivalent summary statistics, the output files from the study-level analysis of one package cannot be directly used to perform meta-analysis in another package. RESULTS: We developed a computationally efficient software program, PreMeta, to resolve the non-compatibility of the four software packages and to facilitate meta-analysis of large-scale sequencing studies in a consortium setting. PreMeta reformats the output files of study-level summary statistics generated by the four packages (text files produced by MASS and RAREMETAL, binary files produced by MetaSKAT, and R data files produced by seqMeta) and translates the summary statistics from one form to another, such that the summary statistics from any package can be used to perform meta-analysis in any other package. With this tool, consortium members are not required to use the same software for study-level analyses. In addition, PreMeta checks for allele mismatches, corrects summary statistics, and allows the rescaled inverse normal transformation to be performed at the meta-analysis stage by rescaling summary statistics. CONCLUSIONS: PreMeta processes summary statistics from the four packages to make them compatible and avoids the need to redo study-level analyses. PreMeta documentation and executable are available at: http://dlin.web.unc.edu/software/premeta. BioMed Central 2017-02-14 /pmc/articles/PMC5310051/ /pubmed/28196472 http://dx.doi.org/10.1186/s12864-017-3573-1 Text en © The Author(s) 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Software Tang, Zheng-Zheng Bunn, Paul Tao, Ran Liu, Zhouwen Lin, Dan-Yu PreMeta: a tool to facilitate meta-analysis of rare-variant associations |
title | PreMeta: a tool to facilitate meta-analysis of rare-variant associations |
title_full | PreMeta: a tool to facilitate meta-analysis of rare-variant associations |
title_fullStr | PreMeta: a tool to facilitate meta-analysis of rare-variant associations |
title_full_unstemmed | PreMeta: a tool to facilitate meta-analysis of rare-variant associations |
title_short | PreMeta: a tool to facilitate meta-analysis of rare-variant associations |
title_sort | premeta: a tool to facilitate meta-analysis of rare-variant associations |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5310051/ https://www.ncbi.nlm.nih.gov/pubmed/28196472 http://dx.doi.org/10.1186/s12864-017-3573-1 |
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