• Genomics & Informatics
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• v.16 no.4
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• pp.37.1-37.3
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• 2018

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.

• Korean Journal of Agricultural and Forest Meteorology
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• v.21 no.2
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• pp.97-109
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• 2019

Degree days have been determined using temperature data measured at nearby weather stations to a site of interest to produce information for supporting decision-making on agricultural production. Alternatively, the data products of Moderate Resolution Imaging Spectroradiometer (MODIS) can be used for estimation of degree days in a given region, e.g., Korean Peninsula. The objective of this study was to develop a simple tool for processing the MODIS product for estimating cooling degree days (CDD), which would help assessment of heat stress conditions for a crop as well as energy requirement for greenhouses. A set of scripts written in R was implemented to obtain temperature profile data for the region of interest. These scripts had functionalities for processing spatial data, which include reprojection, mosaicking, and cropping. A module to extract air temperature at the surface pressure level was also developed using R extension packages such as rgdal and RcppArmadillo. Random forest (RF) models, which estimate mean temperature and CDD with a different set of MODIS data, were trained at 34 sites in South Korea during 2009 - 2018. Then, the values of CDD were calculated over Korean peninsula during the same period using those RF models. It was found that the CDD estimates using the MODIS data explained >74% of the variation in the CDD measurements at the weather stations in North Korea as well as South Korea. These results indicate that temperature data derived from the MODIS atmospheric products would be useful for reliable estimation of CDD. Our results also suggest that the MODIS data can be used for preparation of weather input data for other temperature-based agro-ecological models such as growing degree days or chill units.