Molecular Concepts (Gene Sets) prepared at VAI

Description

A few gene sets compiled at VAI. We have found useful in our analysis.

Usage

data(VAIgsc)

Format

The format is: chr "VAIgsc"

Source

Various sources... See individual objects for PMID, GEO accession, etc..

Examples

data(VAIgsc)
summary(VAIgsc)
details(VAIgsc[[1]])

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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/VAIgsc.Rd_%03d_medium.png", width=480, height=480)
> ### Name: VAIgsc
> ### Title: Molecular Concepts (Gene Sets) prepared at VAI
> ### Aliases: VAIgsc
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(VAIgsc)
> summary(VAIgsc)
Loading required package: GSEABase
Loading required package: annotate
Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

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

    addNode

                        Length Class   Mode
CMYC.1 down             1      GeneSet S4  
CMYC.1 up               1      GeneSet S4  
E2F3.1 down             1      GeneSet S4  
E2F3.1 up               1      GeneSet S4  
HRAS.1 down             1      GeneSet S4  
HRAS.1 up               1      GeneSet S4  
SRC.1 down              1      GeneSet S4  
SRC.1 up                1      GeneSet S4  
BRAF.1 up               1      GeneSet S4  
BRAF.1 down             1      GeneSet S4  
ES.M.1 UP               1      GeneSet S4  
ES.M.1 DOWN             1      GeneSet S4  
FH.1 UP                 1      GeneSet S4  
FH.1 DOWN               1      GeneSet S4  
HGF.2 UP                1      GeneSet S4  
HGF.2 DOWN              1      GeneSet S4  
HYPEROXIA.1 UP          1      GeneSet S4  
HYPEROXIA.1 DOWN        1      GeneSet S4  
HYPEROXIA.2 UP          1      GeneSet S4  
HYPEROXIA.2 DOWN        1      GeneSet S4  
HYPOXIA.1 UP.big        1      GeneSet S4  
HYPOXIA.1 UP.small      1      GeneSet S4  
HYPOXIA.1 DOWN          1      GeneSet S4  
MET.3 up                1      GeneSet S4  
Chromosomal Instability 1      GeneSet S4  
NFKB1.2 down            1      GeneSet S4  
NFKB1.2 up              1      GeneSet S4  
TNF.2 down              1      GeneSet S4  
TNF.2 up                1      GeneSet S4  
TNF.1 up                1      GeneSet S4  
TNF.1 down              1      GeneSet S4  
NFKB1.1 up              1      GeneSet S4  
NFKB1.1 down            1      GeneSet S4  
VEGF.1 up               1      GeneSet S4  
VEGF.1 down             1      GeneSet S4  
WND.1 UP                1      GeneSet S4  
WND.1 DOWN              1      GeneSet S4  
> details(VAIgsc[[1]])
setName: CMYC.1 down 
geneIds: 27, 101, ..., 377582 (total: 89)
geneIdType: EntrezId
collectionType: ExpressionSet 
setIdentifier: 185b7a75-038d-4a5e-c498-d25297d24c9d
description: 
organism: 
pubMedIds: 16273092
urls: 
contributor: Karl Dykema <karl.dykema@vai.org>
setVersion: 0.0.1
creationDate: Fri Sep 14 12:00:24 2007
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>