Dinh/Dinh 2015/NOTES/2016-2-15: Difference between revisions

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(Created page with "==Twin MZ Analysis== ===(1) make methylation matrices & perform smoothing with bsseq=== * Smoothing parameters: number of sites (ns = 70), window size (h=1000) ===(2) Computin...")
 
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==Twin MZ Analysis==
==Twin MZ Analysis==
===(1) make methylation matrices & perform smoothing with bsseq===
===(1) make methylation matrices & perform smoothing with bsseq===
* Methylation sites: minimum 4 samples with 3x depth of coverage per site.
* Smoothing parameters: number of sites (ns = 70), window size (h=1000)
* Smoothing parameters: number of sites (ns = 70), window size (h=1000)
===(2) Computing the T-statistics===
===(2) Computing the T-statistics===

Revision as of 01:49, 16 February 2016

Twin MZ Analysis

(1) make methylation matrices & perform smoothing with bsseq

  • Methylation sites: minimum 4 samples with 3x depth of coverage per site.
  • Smoothing parameters: number of sites (ns = 70), window size (h=1000)

(2) Computing the T-statistics

  • Bsseq doesn't allow for paired samples T-test.
  • Calculate the T-statistics and then perform segmentation to obtain DMRs

(3) Visualize DMRs

  • Hclustering