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TODOs.Rmd
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TODOs.Rmd
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---
title: "TODOs"
author: "Peter Hickey"
date: `r Sys.Date()`
output: html_document
---
# TODOs
## Confirm validity of "2" classes and methods
Confirm that the new "2" classes (e.g., `SimulateMethylome2`, `SimualteBSParam2`) and methods (`simulate2()`) work as intended.
- [x] Empirical co-methylation model
- [x] $\beta$-values.
- __Looks great.__
- [x] Correlation of $\beta$-values.
- __Way too correlated.__
- [x] Within-fragment co-methylation.
- __Looks pretty good, probably upwardly biased due to inherent bias in LOR with small $d$ and extreme `marginalProb`.__
- [x] Empirical co-methylation model with perturbed `marginalProb`.
- [x] $\beta$-values.
- __Looks great.__
- [x] Correlation of $\beta$-values.
- __Reduced from above, but still probably too correlated.__
- [x] Within-fragment co-methylation.
- __Looks pretty good, probably upwardly biased due to inherent bias in LOR with small $d$ and extreme `marginalProb`.__
- [x] Independence model, i.e., $LOR = 0$ uniformly.
- [x] $\beta$-values.
- __Looks great.__
- [x] Correlation of $\beta$-values.
- __Way too correlated.__
- [x] Within-fragment co-methylation.
- __Looks pretty good, approximately flat as a function of $IPD$. However, there is clear evidence of bias because $LOR \approx 1$ meaning $OR \approx 2^1 = 2$.__
- [x] Independence model, i.e., $LOR = 0$ uniformly, with perturbed `marginalProb`
- [x] $\beta$-values.
- __Looks great.__
- [x] Correlation of $\beta$-values.
- __Reduced from above, but still probably too correlated.__
- [x] Within-fragment co-methylation.
- __Looks pretty good, probably upwardly biased due to inherent bias in LOR with small $d$ and extreme `marginalProb`.__
Once confirmed, deprecate the old "1" classes and methods in favour of the "2" classes and methods.
__UP TO HERE__
- [ ] Classes and methods deprecated.