Last updated: 2024-05-22
Checks: 0 1
Knit directory: RA_Tcell_omics/analysis/
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Focused analysis of the
methylation array data (no X or Y chromoses)
In this analysis, probes on sex chromosomes are removed and no blocking
was used in the hypothesis testing.
Focused analysis
of the methylation array data (with X chromosome, but not Y
chromosome)
In this analysis, both male and female samples are used. Sex was blocked
in the hypothesis testing to avoid bias.
Focused analysis
of the methylation array data (only X chromosome)
In this analysis, both male and female samples are used. Male
samples were removed during the hypothesis testing but included in the
visualization.
Focused analysis
of the methylation array data (only Y chromosome in male
samples)
Note that after filtering for probes on Y chromosome in male samples,
there are only 3 Controls and 2 RA samples left. So the results may be
unreliable.
Differential methylated region
(DMR) analysis
In this analysis, DMR analysis was used to identified differentially
methylated regions related to gene regulatory elements, e.g. promoters,
enhancers and so on.