GEM package : methodologies to discovery associations among DNA methylation (M), genetic variation (G) and environmental influences (E)

Epigenetics is the process of heritable change in an organism’s phenotype that is not caused by heritable genetic factors. DNA methylation and Histone modifications are some of the most widely studied epigenetic changes. It has long been known that epigenetic changes are caused by environmental fact...

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Main Author: Heng, Edmund Kai Yang
Other Authors: Kwoh Chee Keong
Format: Final Year Project
Language:English
Published: 2015
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Online Access:http://hdl.handle.net/10356/62833
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Institution: Nanyang Technological University
Language: English
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spelling sg-ntu-dr.10356-628332023-03-03T20:45:16Z GEM package : methodologies to discovery associations among DNA methylation (M), genetic variation (G) and environmental influences (E) Heng, Edmund Kai Yang Kwoh Chee Keong School of Computer Engineering A*STAR Institute for Clinical Sciences (SICS) DRNTU::Engineering::Computer science and engineering::Computer applications::Life and medical sciences DRNTU::Engineering::Computer science and engineering::Software::Software engineering Epigenetics is the process of heritable change in an organism’s phenotype that is not caused by heritable genetic factors. DNA methylation and Histone modifications are some of the most widely studied epigenetic changes. It has long been known that epigenetic changes are caused by environmental factors. These changes can regulate genes and may result in diseases such as cancer. GEM is an R software suite that seeks to associate genetic and environmental factors with the epigenetic changes in an effort to contribute to Epigenetic Wide Association Studies (EWAS). Part of that goal includes the assembly of DNA methylation processing and analysis functions, providing researchers with the computational methodologies to further explore the relationship between DNA methylation and genetic and environmental interactions. This project aims to contribute to the EWAS cause, as well as researchers in the epigenetics research community, by packaging the existing R methylation association methodologies into an R package that is GEM. This involved the analysis of existing scripts for restructure and documentation into required the package format as well as possible optimization and error correction. Due to the specificity of existing GEM methodologies, restructuring for scalability and extensibility could not be achieved. Additionally, the issue of efficiency has to be taken into consideration due to the long runtime of some scripts. In order to improve runtime of the GEM analysis, it is recommended that the use of parallel processing or external C language scripts be considered. Also, greater insight into the domain of biology and epigenetics would likely be helpful in the process of restructuring for scalability and extensibility. Bachelor of Engineering (Computer Science) 2015-04-29T08:47:35Z 2015-04-29T08:47:35Z 2015 2015 Final Year Project (FYP) http://hdl.handle.net/10356/62833 en Nanyang Technological University 89 p. application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic DRNTU::Engineering::Computer science and engineering::Computer applications::Life and medical sciences
DRNTU::Engineering::Computer science and engineering::Software::Software engineering
spellingShingle DRNTU::Engineering::Computer science and engineering::Computer applications::Life and medical sciences
DRNTU::Engineering::Computer science and engineering::Software::Software engineering
Heng, Edmund Kai Yang
GEM package : methodologies to discovery associations among DNA methylation (M), genetic variation (G) and environmental influences (E)
description Epigenetics is the process of heritable change in an organism’s phenotype that is not caused by heritable genetic factors. DNA methylation and Histone modifications are some of the most widely studied epigenetic changes. It has long been known that epigenetic changes are caused by environmental factors. These changes can regulate genes and may result in diseases such as cancer. GEM is an R software suite that seeks to associate genetic and environmental factors with the epigenetic changes in an effort to contribute to Epigenetic Wide Association Studies (EWAS). Part of that goal includes the assembly of DNA methylation processing and analysis functions, providing researchers with the computational methodologies to further explore the relationship between DNA methylation and genetic and environmental interactions. This project aims to contribute to the EWAS cause, as well as researchers in the epigenetics research community, by packaging the existing R methylation association methodologies into an R package that is GEM. This involved the analysis of existing scripts for restructure and documentation into required the package format as well as possible optimization and error correction. Due to the specificity of existing GEM methodologies, restructuring for scalability and extensibility could not be achieved. Additionally, the issue of efficiency has to be taken into consideration due to the long runtime of some scripts. In order to improve runtime of the GEM analysis, it is recommended that the use of parallel processing or external C language scripts be considered. Also, greater insight into the domain of biology and epigenetics would likely be helpful in the process of restructuring for scalability and extensibility.
author2 Kwoh Chee Keong
author_facet Kwoh Chee Keong
Heng, Edmund Kai Yang
format Final Year Project
author Heng, Edmund Kai Yang
author_sort Heng, Edmund Kai Yang
title GEM package : methodologies to discovery associations among DNA methylation (M), genetic variation (G) and environmental influences (E)
title_short GEM package : methodologies to discovery associations among DNA methylation (M), genetic variation (G) and environmental influences (E)
title_full GEM package : methodologies to discovery associations among DNA methylation (M), genetic variation (G) and environmental influences (E)
title_fullStr GEM package : methodologies to discovery associations among DNA methylation (M), genetic variation (G) and environmental influences (E)
title_full_unstemmed GEM package : methodologies to discovery associations among DNA methylation (M), genetic variation (G) and environmental influences (E)
title_sort gem package : methodologies to discovery associations among dna methylation (m), genetic variation (g) and environmental influences (e)
publishDate 2015
url http://hdl.handle.net/10356/62833
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