Prediction of DNA methylation state of MGMT promoter based on HM-450K and HM-27K infinium platforms
## Description ##
This R package contains function to compute the prediction of the DNA methylation of MGMT promoter with data from infinium HM-450K and HM-27K platforms
**NOTA:** This version is a beta version! as results, the R package mgmtstp27 is still in development and the documentation need some corrections (e.g. language, etc ...).
## Installation ##
To install this package, load the archive containing the package mgmtstp27 (see below), start R and enter:
The sources are avalaible [here](https://code.google.com/p/mgmtstp27/source/browse/#git%2Ftrunk%2FRpackage).
Additional documentation is avaialble [here](https://code.google.com/p/mgmtstp27/source/browse/#git%2Ftrunk%2FRdoc):
* Introduction to R package mgmtstp27 (version 0.1, in preparation, intromgmtstp27.pdf)
* Effect of normalization on the prediction of DNA methylation status of MGMT promoter: example with HM-450K Infinium data from TCGA and the R package mgmtstp27 (version 0.1, in preparation, docmgmtstp27.pdf)
* Prediction of the DNA methylation of MGMT with raw data (format IDAT) from HM-27k (version 0.1, in preparation, MgmtPredTCGA.pdf)
## Unexhaustive References ##
* Bady, P., D. Sciuscio, A.-C. Diserens, J. Bloch, M. J. van den Bent, C. Marosi, P.-Y. Dietrich, M. Weller, L. Mariani, F. L. Heppner, D. R. McDonald, D. Lacombe, R. Stupp, M. Delorenzi, and M. E. Hegi. (2012). MGMT methylation analysis of glioblastoma on the Infinium methylation BeadChip identifies two distinct CpG regions associated with gene silencing and outcome, yielding a prediction model for comparisons across datasets, tumor grades, and CIMP-status. Acta Neuropathologica 124:547-560. PubMed:http://www.ncbi.nlm.nih.gov/pubmed/22810491
