MM2S: Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Version 1.0.5

Description: A single-sample classifier that generates Medulloblastoma (MB) subtype predictions for single-samples of human MB patients and model systems, including cell lines and mouse-models. The MM2S algorithm uses a systems-based methodology that facilitates application of the algorithm on samples irrespective of their platform or source of origin. MM2S demonstrates > 96% accuracy for patients of well-characterized normal cerebellum, Wingless (WNT), or Sonic hedgehog (SHH) subtypes, and the less-characterized Group4 (86%) and Group3 (78.2%). MM2S also enables classification of MB cell lines and mouse models into their human counterparts.This package contains function for implementing the classifier onto human data and mouse data, as well as graphical rendering of the results as PCA plots and heatmaps.

Browse man pages Browse package API and functions Browse package files

AuthorDeena M.A. Gendoo <deena.gendoo@utoronto.ca>, Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Bioconductor views Cancer Classification MM2Sdata Microarray Software Visualization
Date of publication2016-02-25 00:39:19
MaintainerDeena M.A. Gendoo <deena.gendoo@utoronto.ca>
LicenseGPL-3
Version1.0.5
URL http://www.sciencedirect.com/science/article/pii/S0888754315000774 http://www.pmgenomics.ca/bhklab/software/mm2s
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("MM2S")

Man pages

GTML_Mouse_Preds: Table of Pre-computed MM2S Predictions for 32 replicates of...
Human_Cho_Expr: Gene Expression data from selected samples of the Human CHO...
MM2S.human: MM2S Prediction of Human Medulloblastoma Samples
MM2S.mouse: MM2S Prediction of Mouse Medulloblastoma Samples
MM2Ssetup: MM2S ssGSEA Training Matrix, MB Sample Group information for...
PCARender: PCA Projections of ssGSEA Rank Matrix for Test Samples Onto...
PredictionsBarplot: Stacked Barplot of MM2S Subtype Predictions for Given Samples
PredictionsDistributionBoxplot: Boxplot of MM2S Subtype Predictions for Given Samples
PredictionsDistributionPie: Heatmap of MM2S Subtype Predictions for Given Samples
PredictionsHeatmap: Heatmap of MM2S Subtype Predictions for Given Samples
WNT_Mouse_Expr: Gene Expression data pertaining to the GMTL mouse mode

Functions

Frozen_ES_Rank_Matrix Man page
GTML_Mouse_Preds Man page
GenesetStatGroup3 Man page
GenesetStatGroup4 Man page
GenesetStatNormal Man page
GenesetStatSHH Man page
GenesetStatWNT Man page
HumanGMT Man page
Human_Cho_Expr Man page
MB_SampleInfo Man page
MM2S.human Man page Source code
MM2S.mouse Man page Source code
MM2Ssetup Man page
MouseGMT Man page
PCARender Man page Source code
PredictionsBarplot Man page Source code
PredictionsDistributionBoxplot Man page Source code
PredictionsDistributionPie Man page Source code
PredictionsHeatmap Man page Source code
WNT_Mouse_Expr Man page
genesetHuman Man page

Files

inst
inst/doc
inst/doc/MM2S.Rnw
inst/doc/MM2S_FromRawData.pdf
inst/doc/MM2S_FromRawData.R
inst/doc/MM2S_Vignette_FrozenCapture.pdf
inst/doc/MM2S.pdf
inst/doc/MM2S_FromRawData.Rnw
inst/doc/MM2S_FromRawData_Vignette_FrozenCapture.pdf
inst/doc/MM2S.R
NAMESPACE
NEWS
data
data/MM2Ssetup.rda
data/WNT_Mouse_Expr.rda
data/Human_Cho_Expr.rda
data/datalist
data/GTML_Mouse_Preds.rda
R
R/MM2S.mouse.R
R/PredictionsDistributionBoxplot.R
R/PredictionsDistributionPie.R
R/PCARender.R
R/MM2S.human.R
R/PredictionsHeatmap.R
R/PredictionsBarplot.R
vignettes
vignettes/MM2S.Rnw
vignettes/MM2S_FromRawData.Rnw
MD5
README
build
build/vignette.rds
DESCRIPTION
man
man/MM2Ssetup.Rd
man/GTML_Mouse_Preds.Rd
man/MM2S.human.Rd
man/PredictionsDistributionPie.Rd
man/WNT_Mouse_Expr.Rd
man/PredictionsDistributionBoxplot.Rd
man/PredictionsHeatmap.Rd
man/MM2S.mouse.Rd
man/Human_Cho_Expr.Rd
man/PredictionsBarplot.Rd
man/PCARender.Rd
MM2S documentation built on May 19, 2017, 5:29 p.m.