Table 11.
Comparison of some features of the methods for cell-type mixture adjustment
| Method | Phen. allowed a | Input values b | K c | Link |
|---|---|---|---|---|
| Ref-based | Any | Beta | N/A | http://people.oregonstate.edu/~housemae/software/TutorialLondon2014 |
| http://bioconductor.org/packages/release/bioc/html/minfi.html | ||||
| Ref-free | Any | Beta | Estimated | http://cran.r-project.org/web/packages/RefFreeEWAS/index.html |
| SVA | Any | Beta or logit(beta) | Estimated | http://bioconductor.org/packages/release/bioc/html/sva.html |
| ISVA | Continuous | Beta or logit(beta) | Estimated | http://cran.r-project.org/web/packages/isva/index.html |
| EWASher | Binary | Beta | Estimated | http://research.microsoft.com/en-us/downloads/472fe637-7cb9-47d4-a0df-37118760ccd1 |
| CellCDec | Not used | Beta | Input | https://github.com/jameswagner/CellCDec |
| Deconf | Not used | Beta or logit(beta) | Input | http://web.cbio.uct.ac.za/~renaud/CRAN |
| RUV | Any | Beta or logit(beta) | Estimated | https://cran.r-project.org/web/packages/ruv/index.html |
aWhat kinds of phenotype are allowed?
bDoes the method use methylation proportions (beta values)? Or logit transformed beta values?
cDoes the method estimate the number of latent cell types K, or is K input into the algorithm?