varPro (version 1.0.1)

gliomas: Diffuse Adult Glioma

Description

Subset of the data used in Ceccarelli et al. (2016) for molecular profiling of adult diffuse gliomas. As part of the analysis, the authors developed a supervised analysis using DNA methylation data. Their original dataset was collected from a core set of 25,978 CpG probes which was reduced to eliminate sites that were methylated. This reduced set of 1206 probes from 880 tissues makes up part of the features of this data. Also included are clinical data and other molecular data collected for the samples. The outcome is a supervised class label developed in the study with labels: Classic-like, Codel, G-CIMP-high, G-CIMP-low, LGm6-GBM, Mesenchymal-like and PA-like.

References

Ceccarelli, M., Barthel, F.P., Malta, T.M., Sabedot, T.S., Salama, S.R., Murray, B.A., Morozova, O., Newton, Y., Radenbaugh, A., Pagnotta, S.M. et al. (2016). Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma. Cell, 164, 550-563.

Examples

# \donttest{
data(glioma, package = "varPro")
o <- varpro(y~., glioma, nodesize=2, max.tree=250)
imp <- importance(o)
print(head(imp$unconditional))
print(imp$conditional.z)
# }