MethylDetectR - A Translational Tool for Methylation-Based Health Profiling

This dataset includes reproducible code for the two applications related to the 'MethylDetectR' software. These .R files are included as 'MethylDetectR - Calculate Your Scores.R' and 'MethylDetectR.R'. An example DNAm file and Sexinfo file for upload to 'MethylDetectR - Calculate Your Scores' are included. These are 'DNAm_File_Example.rds' and 'Sexinfo_example.csv', respectively. An example output file from this application/for upload to 'MethylDetectR' is included as 'MethylDetectR - Test For Upload.csv'. Furthermore, a script for the user to generate their own DNAm-based estimated values for human traits is included as 'Script_For_User_To_Generate_Scores.R'. A necessary associated file as 'Predictors_Shiny_By_Groups.csv' is also present for the script to run. Lastly, coefficients for lifestyle traits and HDL cholesterol are attached as 'Lifestyle_Biochemical_LASSO_Coefficients.xlsx'. These coefficients are separate from those included in the original McCartney and Hillary et al (2018) publication in <em>Genome Biology</em>. The reason for this difference is that the attached coefficients are generated from scaled DNAm data.本数据集包含与"MethylDetectR"软件相关的两款应用的可复现代码。这些.R脚本文件分别命名为"MethylDetectR - Calculate Your Scores.R"与"MethylDetectR.R"。 本数据集还提供了两份可上传至"MethylDetectR - Calculate Your Scores"的示例文件：分别为DNA甲基化（DNAm）数据文件与性别信息文件，对应文件名依次为"DNAm_File_Example.rds"与"Sexinfo_example.csv"。 另有一份可由该应用生成或用于上传至"MethylDetectR"的示例输出文件，文件名为"MethylDetectR - Test For Upload.csv"。 此外，本数据集还附带了一份供用户自行生成人类性状DNA甲基化估算值的脚本文件"Script_For_User_To_Generate_Scores.R"，该脚本运行所需的配套必要文件"Predictors_Shiny_By_Groups.csv"亦一同包含在内。 最后，本数据集还附带了生活方式性状与高密度脂蛋白（High-Density Lipoprotein, HDL）胆固醇相关的套索（LASSO）回归系数文件"Lifestyle_Biochemical_LASSO_Coefficients.xlsx"。该系数集与McCartney与Hillary等人2018年发表于《Genome Biology》的原始研究中所使用的系数并不相同，二者存在差异的原因在于，本次附带的系数源自经过标准化处理的DNA甲基化数据。