TcgaGBM: Glioblastoma multiforme gene expression data

In HCsnip: Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree

Description

The subset of latest version of TCGA glioblastoma (GBM) level 3 gene expression data with partial clinical info. Contains expression profiles of 120 samples measured on 3000 genes. Clinical data includes follow-up and type of drugs patients have been administered.

Usage

data(TcgaGBM)

Format

An object of list class

Note

The complete dataset is available at the TCGA data portal https://tcga-data.nci.nih.gov/tcga/.

Source

The Cancer Genome Atlas Network (2008), "Comprehensive genomic characterisation defines human glioblastoma genes and core pathways", Nature, 490, 61-70.

Examples

data(TcgaGBM)
names(TcgaGBM)

Example output

Loading required package: survival
Loading required package: coin
Loading required package: fpc
Loading required package: clusterRepro
Loading required package: impute
Loading required package: randomForestSRC

 randomForestSRC 2.8.0 
 
 Type rfsrc.news() to see new features, changes, and bug fixes. 
 

Loading required package: sm
Package 'sm', version 2.2-5.6: type help(sm) for summary information
Loading required package: sigaR
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: CGHbase
Loading required package: marray
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: mvtnorm
Warning message:
no DISPLAY variable so Tk is not available 
[1] "em"        "surv.time" "status"    "drugs"    

HCsnip documentation built on Nov. 17, 2017, 11:17 a.m.