DNA Methylation Sequencing Analysis
  • Introduction
  • Data Preparation
    • Locate the MethPipe Files
    • Download Utilities
    • Download Annotations
    • Annotation File Preparation – Defining Genomic Regions
  • Analysis Work Flow
    • DNA Methylation at Genomic Bins
    • DNA Methylation at CpG Islands
    • DNA Methylation at TFBS
    • DNA Methylation at Various Genic Structure Regions
    • DNA Methylation at Repeat Elements
    • Add CpG Islands Co-localization Information to HMR BED Files
    • Similarity and Differences of HMRs and PMDs from H1 and IMR90
      • HMRs
      • PMDs
  • Visualization Using R
    • Install R Libraries
    • Execute the R Scripts
  • An introduction of UCSC Genome Browser
    • General Usage
    • The Compressed Binary Index Format
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Visualization Using R

In the this chapter, we will demonstrate how to use the methylation information produced in Chapter 2 to produce figures that aids in our exploration of the methylation patterns in these two cell lines.

For reader who do not have an account on the ALPS server, please check if you have access to the R environment for statistical analysis in your computer or server. If not, please download and compile the software.

wget http://cran.csie.ntu.edu.tw/src/base/R-3/R-3.1.2.tar.gz
tar zxfv R-3.1.2.tar.gz
cd R-3.1.2
./configure
make

R is also available on many operating system, including Windows. Please visit its website at http://www.r-project.org/.

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Last updated 5 years ago

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