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