Title
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:
install.packages("mgmtstp27_0.6.tar.gz",repos=NULL)
install.packages("mgmtstp27_0.6.zip",repos=NULL)The sources are avalaible here.
Additional documentation is avaialble here:
- 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
Depends
R (>= 3.1.2), minfi, lumi, ade4,methylumi,MASS R (>= 3.2.0), minfi, lumi, ade4,methylumi,MASS
Suggests
boot
License
GPL version 2 or newer
Date
2014-09-11
Revison
2015-06-16
Version
alpha 0.6 (beta version for R-3.1.2) alpha 0.6-2 (beta version for R-3.2.0)