Custom Clusters

Description

Matrix containing a set of drugs and their corresponding clusters which can be used as input to the classifyprofile function.

Usage

data(customClust)

Format

Data frame with 47 rows and 2 columns. Columns are headed "Drug" and "Cluster".

Details

Each row refers to a compound in the customDB data set link{customDB} with its corresponding cluster assignment in the second column. These profiles are a subset of the Connectivity Map data [1] (full set available in the DrugVsDiseasedata package DrugVsDiseasedata, data object drugRL, for example use. Clusters were generated using affinity propagation clustering [2]

Source

http://www.broadinstitute.org/cmap/

References

[1] Lamb J et~al. (2006) The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease. Science, 313(5795), 1929-1935. [2] U. Bodenhofer, A. Kothmeier, and S. Hochreiter. APCluster: an R package for affinity propagation clustering. Bioinformatics, 27(17):2463-2464, 2011.

Examples

data(customClust)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(DrugVsDisease)
Loading required package: affy
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: biomaRt
Loading required package: ArrayExpress
Loading required package: GEOquery
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: DrugVsDiseasedata
Loading required package: cMap2data

Attaching package: 'cMap2data'

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

    genelist

Loading required package: qvalue
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DrugVsDisease/customClust.rd_%03d_medium.png", width=480, height=480)
> ### Name: customClust
> ### Title: Custom Clusters
> ### Aliases: customClust
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(customClust)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>