Genome-wide DMP analysis - Githubissues

FoxoTech / methylize

Python-based Illumina methylation array analysis software

MIT License

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Genome-wide DMP analysis #1

Closed brianchengithub closed 5 years ago

brianchengithub commented 6 years ago

Outputs

Table of associations (CSV file) Rows = probes Columns = ...

[x] regression coefficient
[x] SE
[x] 95% Confidence Interval (Upper Limit)
[x] 95% Confidence Interval (Lower Limit)
[x] p-value
[x] FDR

Volcano plot

[x] x-axis = regression coefficient
[x] y-axis = -log10(pvalue)
[x] Draw horizontal lines at genome-wide significance levels (p=5E-8 and FDR<0.05)

Manhattan plot

[x] Color coded by chromosome
[x] Draw horizontal lines at genome-wide significance levels (p=5E-8 and FDR<0.05)

brianchengithub commented 6 years ago

[ ] Use GLM to allow for linear, logistic, and Cox regression.
[ ] Allow user to specify list of fixed effects (i.e., column names in their phenotype file).
[ ] Allow user to specify list of random effects (i.e., column names in their phenotype file).