EFMDR-Fast: An Application of Empirical Fuzzy Multifactor Dimensionality Reduction for Fast Execution
Gene-gene interaction is a key factor for explaining missing heritability. Many methods have been proposed to identify gene-gene interactions. Multifactor dimensionality reduction (MDR) is a well-known method for the detection of gene-gene interactions by reduction from genotypes of single-nucleotid...
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BioMed Central
2018-12-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2018-16-4-e37.pdf |
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| author | Sangseob Leem Taesung Park |
| author_facet | Sangseob Leem Taesung Park |
| author_sort | Sangseob Leem |
| collection | DOAJ |
| description | Gene-gene interaction is a key factor for explaining missing heritability. Many methods have been proposed to identify gene-gene interactions. Multifactor dimensionality reduction (MDR) is a well-known method for the detection of gene-gene interactions by reduction from genotypes of single-nucleotide polymorphism combinations to a binary variable with a value of high risk or low risk. This method has been widely expanded to own a specific objective. Among those expansions, fuzzy-MDR uses the fuzzy set theory for the membership of high risk or low risk and increases the detection rates of gene-gene interactions. Fuzzy-MDR is expanded by a maximum likelihood estimator as a new membership function in empirical fuzzy MDR (EFMDR). However, EFMDR is relatively slow, because it is implemented by R script language. Therefore, in this study, we implemented EFMDR using RCPP (c++ package) for faster executions. Our implementation for faster EFMDR, called EMMDR-Fast, is about 800 times faster than EFMDR written by R script only. |
| format | Article |
| id | doaj-art-eeaefacdf0e6477f9377d78c34242999 |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2018-12-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-eeaefacdf0e6477f9377d78c342429992025-02-02T04:14:06ZengBioMed CentralGenomics & Informatics2234-07422018-12-0116410.5808/GI.2018.16.4.e37539EFMDR-Fast: An Application of Empirical Fuzzy Multifactor Dimensionality Reduction for Fast ExecutionSangseob LeemTaesung ParkGene-gene interaction is a key factor for explaining missing heritability. Many methods have been proposed to identify gene-gene interactions. Multifactor dimensionality reduction (MDR) is a well-known method for the detection of gene-gene interactions by reduction from genotypes of single-nucleotide polymorphism combinations to a binary variable with a value of high risk or low risk. This method has been widely expanded to own a specific objective. Among those expansions, fuzzy-MDR uses the fuzzy set theory for the membership of high risk or low risk and increases the detection rates of gene-gene interactions. Fuzzy-MDR is expanded by a maximum likelihood estimator as a new membership function in empirical fuzzy MDR (EFMDR). However, EFMDR is relatively slow, because it is implemented by R script language. Therefore, in this study, we implemented EFMDR using RCPP (c++ package) for faster executions. Our implementation for faster EFMDR, called EMMDR-Fast, is about 800 times faster than EFMDR written by R script only.http://genominfo.org/upload/pdf/gi-2018-16-4-e37.pdfEFMDRFuzzy-MDRgene-gene interactionmulti-factor dimensionality reductionRCPP |
| spellingShingle | Sangseob Leem Taesung Park EFMDR-Fast: An Application of Empirical Fuzzy Multifactor Dimensionality Reduction for Fast Execution Genomics & Informatics EFMDR Fuzzy-MDR gene-gene interaction multi-factor dimensionality reduction RCPP |
| title | EFMDR-Fast: An Application of Empirical Fuzzy Multifactor Dimensionality Reduction for Fast Execution |
| title_full | EFMDR-Fast: An Application of Empirical Fuzzy Multifactor Dimensionality Reduction for Fast Execution |
| title_fullStr | EFMDR-Fast: An Application of Empirical Fuzzy Multifactor Dimensionality Reduction for Fast Execution |
| title_full_unstemmed | EFMDR-Fast: An Application of Empirical Fuzzy Multifactor Dimensionality Reduction for Fast Execution |
| title_short | EFMDR-Fast: An Application of Empirical Fuzzy Multifactor Dimensionality Reduction for Fast Execution |
| title_sort | efmdr fast an application of empirical fuzzy multifactor dimensionality reduction for fast execution |
| topic | EFMDR Fuzzy-MDR gene-gene interaction multi-factor dimensionality reduction RCPP |
| url | http://genominfo.org/upload/pdf/gi-2018-16-4-e37.pdf |
| work_keys_str_mv | AT sangseobleem efmdrfastanapplicationofempiricalfuzzymultifactordimensionalityreductionforfastexecution AT taesungpark efmdrfastanapplicationofempiricalfuzzymultifactordimensionalityreductionforfastexecution |