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CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability
Genomic instability is an important hallmark of cancer and more recently has been identified in others like neurodegenrative diseases. Chromosomal instability, as a measure of genomic instability, has been used to characterize clinical and biological phenotypes associated with these diseases by meas...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10143595/ https://www.ncbi.nlm.nih.gov/pubmed/37123011 http://dx.doi.org/10.7717/peerj.15244 |
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author | Oza, Vishal H. Fisher, Jennifer L. Darji, Roshan Lasseigne, Brittany N. |
author_facet | Oza, Vishal H. Fisher, Jennifer L. Darji, Roshan Lasseigne, Brittany N. |
author_sort | Oza, Vishal H. |
collection | PubMed |
description | Genomic instability is an important hallmark of cancer and more recently has been identified in others like neurodegenrative diseases. Chromosomal instability, as a measure of genomic instability, has been used to characterize clinical and biological phenotypes associated with these diseases by measuring structural and numerical chromosomal alterations. There have been multiple chromosomal instability scores developed across many studies in the literature; however, these scores have not been compared because of the lack of a single tool available to calculate and facilitate these various metrics. Here, we provide an R package CINmetrics, that calculates six different chromosomal instability scores and allows direct comparison between them. We also demonstrate how these scores differ by applying CINmetrics to breast cancer data from The Cancer Genome Atlas (TCGA). The package is available on CRAN at https://cran.rproject.org/package=CINmetrics and on GitHub at https://github.com/lasseignelab/CINmetrics. |
format | Online Article Text |
id | pubmed-10143595 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-101435952023-04-29 CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability Oza, Vishal H. Fisher, Jennifer L. Darji, Roshan Lasseigne, Brittany N. PeerJ Computational Biology Genomic instability is an important hallmark of cancer and more recently has been identified in others like neurodegenrative diseases. Chromosomal instability, as a measure of genomic instability, has been used to characterize clinical and biological phenotypes associated with these diseases by measuring structural and numerical chromosomal alterations. There have been multiple chromosomal instability scores developed across many studies in the literature; however, these scores have not been compared because of the lack of a single tool available to calculate and facilitate these various metrics. Here, we provide an R package CINmetrics, that calculates six different chromosomal instability scores and allows direct comparison between them. We also demonstrate how these scores differ by applying CINmetrics to breast cancer data from The Cancer Genome Atlas (TCGA). The package is available on CRAN at https://cran.rproject.org/package=CINmetrics and on GitHub at https://github.com/lasseignelab/CINmetrics. PeerJ Inc. 2023-04-25 /pmc/articles/PMC10143595/ /pubmed/37123011 http://dx.doi.org/10.7717/peerj.15244 Text en ©2023 Oza et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Computational Biology Oza, Vishal H. Fisher, Jennifer L. Darji, Roshan Lasseigne, Brittany N. CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability |
title | CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability |
title_full | CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability |
title_fullStr | CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability |
title_full_unstemmed | CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability |
title_short | CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability |
title_sort | cinmetrics: an r package for analyzing copy number aberrations as a measure of chromosomal instability |
topic | Computational Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10143595/ https://www.ncbi.nlm.nih.gov/pubmed/37123011 http://dx.doi.org/10.7717/peerj.15244 |
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