/Methylation_Analysis

DNA methylation workflow, from beta-values to signatures

Primary LanguageR

Methylation Analysis

DNA methylation workflow, from beta-values to signatures

This workflow contains 4 modules.

  1. Normalization
    • Normalization.R
  2. DMP & DMR
    • DMP_DMR.R
    • 2013Method.R & 2013Method_cv.R
          Test the methods in Exploring genome-wide DNA methylation profiles altered in hepatocellular carcinoma using Infinium HumanMethylation 450 BeadChips. Epigentics 2013.
          By using the methods, the hyper/hypo-methylated sites can be distinguished from DMPs. The dmrcate function was re-defined and the number of hyper/hypo-methylated sites covered by each DMR are also a part of the output now.  
  3. Random Forests
    • RFBoot.R
  4. Lasso
    • Lasso.R

Instructions

  • Requirement of each module can be seen at the beginning of the scripts.
  • Rscripts and data can be found at "/lustre/rdi/user/hantc/tools/Methylation", just copy them to your own directory and test whether it can be run.
  • It is to be noted that packages required by Normalization and DMP_DMR cannot be easily installed on the cluster, so I recommend you to run these 2 modules on your PC.
  • RFBoot takes a long time. Running it on a Cluster is a better option.
  • If the sample size is small, Lasso may return an error.

Change Logs

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2017-12-11

Uploaded new scripts for testing the methods in Exploring genome-wide DNA methylation profiles altered in hepatocellular carcinoma using Infinium HumanMethylation 450 BeadChips. Epigentics 2013.

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2017-12-01

Upload 4 modules.