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mgmtstp27

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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. The R function MGMTpredict directly provides prediction, classification and confidence intervals as illustrated below:

# loading R packages
require(mgmtstp27)
require(minfiData)
# preprocessing of the data
dat <- preprocessRaw(RGsetEx)
# computation of M-value
mvalue <- log2((getMeth(dat)+1)/(getUnmeth(dat)+1))
mvalue <- as.data.frame(t(mvalue))
# predictions
pred1 <- MGMTpredict(mvalue)
head(pred1)
# quality control graphics
par(mfrow=c(2,3))
MGMTqc.pop(pred1,which.plot=1:3,mfrow=NULL)
MGMTqc.single(pred1,nsample=1,which.plot=1:3,mfrow=NULL)

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)

URL