---
title: 'EpipwR.data: Reference data for EpipwR'
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{EpipwR.data: Reference data for EpipwR}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
date: "2024-09-10"
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

EpipwR.data is used to access reference data from ExperimentHub for the EpipwR 
package.

# Data

The data sets accessed through this package are based on source data publicly 
available on the Gene expression omnibus. The authors would like to acknowledge 
the work done by Graw et. al. (2019) in identifying the source data sets for 
EWAS power analyses. EpipwR uses beta distribution parameters $\alpha$,$\beta$, 
estimated through method of moments. Specifically, beta values are calculated 
from the source data set for every subject/CpG combination. Sample means and 
variances are then calculated for each CpG site. Finally, these are converted 
to $\alpha$,$\beta$, using the below formulas:

$\hat{\alpha}=\frac{\bar{x}^2(1-\bar{x})}{s^2}-\bar{x}$

$\hat{\beta}=\frac{\hat{\alpha}(1-\bar{x})}{\bar{x}}$

The below table has access information for each of the source data sets.



|Tissue Type              | Accession Number | Reference                                 |
|-------------------------|------------------|-------------------------------------------|
|Saliva                   | GSE92767         | (Hong et al., 2017)                       |
|Lymphoma                 | GSE42372         | (Matsunaga et al., 2014)                  |
|Placenta                 | GSE62733         | (Kawai et al., 2015)                      |
|Liver                    | GSE61258         | (Horvath et al., 2014)                    |
|Colon                    | GSE77718         | (McInnes et al., 2017)                    |
|Blood (Adults)           | GSE42861         | (Kular et al., 2018; Y. Liu et al., 2013) |
|Blood (Children)         | GSE83334         | (Urdinguio et al., 2016)                  |
|Blood (Newborns)         | GSE82273         | (Markunas et al., 2016)                   |
|Cord-blood (whole blood) | GSE69176         |                                           |
|Cord-blood (PBMC)        | GSE110128        | (Langie et al., 2018)                     |
|Adult (PBMC)             | GSE67170         | (Y. H. Zhang et al., 2018)                |
|Sperm                    | GSE114753        | (Jenkins et al., 2017)                    |



```{r}
# Load sessioninfo package
library(sessioninfo)

# Display session information
session_info()
```

# References

Graw, S., Henn, R., Thompson, J. A., & Koestler, D. C. (2019). pwrEWAS: 
a user-friendly tool for comprehensive power estimation for epigenome wide 
association studies (EWAS). *BMC Bioinformatics*, 20(1), 218--218.