Molecular Concepts prepared at VAI from data created by Golub et al.

Description

386 molecular concepts generated at VAI. The data these concepts were generate from is available from http://www.broad.mit.edu/cmap/.

Usage

data(GOLUBmcs)

Format

a list of "smc" objects

Details

These concepts were generated using the limma BioConductor package. The code used for generation of these concepts is available upon request.

Source

http://www.broad.mit.edu/cmap/

Examples

data(GOLUBmcs)
str(GOLUBmcs[1:4]) 

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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(PGSEA)
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
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: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums


Loading required package: KEGG.db

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

Loading required package: annaffy
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/PGSEA/GOLUBmcs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GOLUBmcs
> ### Title: Molecular Concepts prepared at VAI from data created by Golub et
> ###   al.
> ### Aliases: GOLUBmcs
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(GOLUBmcs)
> str(GOLUBmcs[1:4]) 
List of 4
 $ 12,13-EODE  200 nM  UP                 : list()
  ..- attr(*, "reference")= chr "12,13-EODE  200 nM  UP "
  ..- attr(*, "desc")= chr "UP "
  ..- attr(*, "source")= chr "PubMed"
  ..- attr(*, "design")= chr "????"
  ..- attr(*, "identifier")= chr "17008526"
  ..- attr(*, "species")= chr "human"
  ..- attr(*, "data")= chr "raw"
  ..- attr(*, "private")= chr "no"
  ..- attr(*, "creator")= chr "Karl Dykema <karl.dykema@vai.org>"
  ..- attr(*, "ids")= chr [1:75] "59349" "80129" "7378" "23411" ...
  ..- attr(*, "class")= atomic [1:1] smc
  .. ..- attr(*, "package")= chr "PGSEA"
 $ 12,13-EODE  200 nM  DOWN               : list()
  ..- attr(*, "reference")= chr "12,13-EODE  200 nM  DOWN "
  ..- attr(*, "desc")= chr "DOWN "
  ..- attr(*, "source")= chr "PubMed"
  ..- attr(*, "design")= chr "????"
  ..- attr(*, "identifier")= chr "17008526"
  ..- attr(*, "species")= chr "human"
  ..- attr(*, "data")= chr "raw"
  ..- attr(*, "private")= chr "no"
  ..- attr(*, "creator")= chr "Karl Dykema <karl.dykema@vai.org>"
  ..- attr(*, "ids")= chr [1:75] "515" "6506" "5544" "2766" ...
  ..- attr(*, "class")= atomic [1:1] smc
  .. ..- attr(*, "package")= chr "PGSEA"
 $ 15-delta prostaglandin J2  10 uM  UP   : list()
  ..- attr(*, "reference")= chr "15-delta prostaglandin J2  10 uM  UP "
  ..- attr(*, "desc")= chr "UP "
  ..- attr(*, "source")= chr "PubMed"
  ..- attr(*, "design")= chr "????"
  ..- attr(*, "identifier")= chr "17008526"
  ..- attr(*, "species")= chr "human"
  ..- attr(*, "data")= chr "raw"
  ..- attr(*, "private")= chr "no"
  ..- attr(*, "creator")= chr "Karl Dykema <karl.dykema@vai.org>"
  ..- attr(*, "ids")= chr [1:75] "60" "5478" "6229" "AFFX-hum_alu" ...
  ..- attr(*, "class")= atomic [1:1] smc
  .. ..- attr(*, "package")= chr "PGSEA"
 $ 15-delta prostaglandin J2  10 uM  DOWN : list()
  ..- attr(*, "reference")= chr "15-delta prostaglandin J2  10 uM  DOWN "
  ..- attr(*, "desc")= chr "DOWN "
  ..- attr(*, "source")= chr "PubMed"
  ..- attr(*, "design")= chr "????"
  ..- attr(*, "identifier")= chr "17008526"
  ..- attr(*, "species")= chr "human"
  ..- attr(*, "data")= chr "raw"
  ..- attr(*, "private")= chr "no"
  ..- attr(*, "creator")= chr "Karl Dykema <karl.dykema@vai.org>"
  ..- attr(*, "ids")= chr [1:75] "171392" "5680" "2149" "54557" ...
  ..- attr(*, "class")= atomic [1:1] smc
  .. ..- attr(*, "package")= chr "PGSEA"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>