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Amanida: an R package for meta-analysis of metabolomics non-integral data
SUMMARY: The combination, analysis and evaluation of different studies which try to answer or solve the same scientific question, also known as a meta-analysis, plays a crucial role in answering relevant clinical relevant questions. Unfortunately, metabolomics studies rarely disclose all the statist...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8722753/ https://www.ncbi.nlm.nih.gov/pubmed/34406360 http://dx.doi.org/10.1093/bioinformatics/btab591 |
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author | Llambrich, Maria Correig, Eudald Gumà, Josep Brezmes, Jesús Cumeras, Raquel |
author_facet | Llambrich, Maria Correig, Eudald Gumà, Josep Brezmes, Jesús Cumeras, Raquel |
author_sort | Llambrich, Maria |
collection | PubMed |
description | SUMMARY: The combination, analysis and evaluation of different studies which try to answer or solve the same scientific question, also known as a meta-analysis, plays a crucial role in answering relevant clinical relevant questions. Unfortunately, metabolomics studies rarely disclose all the statistical information needed to perform a meta-analysis. Here, we present a meta-analysis approach using only the most reported statistical parameters in this field: P-value and fold-change. The P-values are combined via Fisher’s method and fold-changes by averaging, both weighted by the study size (n). The amanida package includes several visualization options: a volcano plot for quantitative results, a vote plot for total regulation behaviours (up/down regulations) for each compound, and a explore plot of the vote-counting results with the number of times a compound is found upregulated or downregulated. In this way, it is very easy to detect discrepancies between studies at a first glance. AVAILABILITY AND IMPLEMENTATION: Amanida code and documentation are at CRAN and https://github.com/mariallr/amanida. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-8722753 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-87227532022-01-05 Amanida: an R package for meta-analysis of metabolomics non-integral data Llambrich, Maria Correig, Eudald Gumà, Josep Brezmes, Jesús Cumeras, Raquel Bioinformatics Applications Notes SUMMARY: The combination, analysis and evaluation of different studies which try to answer or solve the same scientific question, also known as a meta-analysis, plays a crucial role in answering relevant clinical relevant questions. Unfortunately, metabolomics studies rarely disclose all the statistical information needed to perform a meta-analysis. Here, we present a meta-analysis approach using only the most reported statistical parameters in this field: P-value and fold-change. The P-values are combined via Fisher’s method and fold-changes by averaging, both weighted by the study size (n). The amanida package includes several visualization options: a volcano plot for quantitative results, a vote plot for total regulation behaviours (up/down regulations) for each compound, and a explore plot of the vote-counting results with the number of times a compound is found upregulated or downregulated. In this way, it is very easy to detect discrepancies between studies at a first glance. AVAILABILITY AND IMPLEMENTATION: Amanida code and documentation are at CRAN and https://github.com/mariallr/amanida. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2021-08-18 /pmc/articles/PMC8722753/ /pubmed/34406360 http://dx.doi.org/10.1093/bioinformatics/btab591 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Applications Notes Llambrich, Maria Correig, Eudald Gumà, Josep Brezmes, Jesús Cumeras, Raquel Amanida: an R package for meta-analysis of metabolomics non-integral data |
title | Amanida: an R package for meta-analysis of metabolomics non-integral data |
title_full | Amanida: an R package for meta-analysis of metabolomics non-integral data |
title_fullStr | Amanida: an R package for meta-analysis of metabolomics non-integral data |
title_full_unstemmed | Amanida: an R package for meta-analysis of metabolomics non-integral data |
title_short | Amanida: an R package for meta-analysis of metabolomics non-integral data |
title_sort | amanida: an r package for meta-analysis of metabolomics non-integral data |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8722753/ https://www.ncbi.nlm.nih.gov/pubmed/34406360 http://dx.doi.org/10.1093/bioinformatics/btab591 |
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