ExpressionSet instance for illustrating integrative smlSet container

Description

ExpressionSet instance for illustrating integrative smlSet container

Usage

data(eset)

Format

The format is: Formal class 'ExpressionSet' [package "Biobase"] with 7 slots ..@ experimentData :Formal class 'MIAME' [package "Biobase"] with 13 slots
.. .. ..@ name : chr ""
.. .. ..@ lab : chr ""
.. .. ..@ contact : chr ""
.. .. ..@ title : chr ""
.. .. ..@ abstract : chr ""
.. .. ..@ url : chr ""
.. .. ..@ pubMedIds : chr ""
.. .. ..@ samples : list()
.. .. ..@ hybridizations : list()
.. .. ..@ normControls : list()
.. .. ..@ preprocessing : list()
.. .. ..@ other : list()
.. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots
.. .. .. .. ..@ .Data:List of 2
.. .. .. .. .. ..$ : int [1:3] 1 0 0
.. .. .. .. .. ..$ : int [1:3] 1 1 0
..@ assayData :<environment: 0x10bf12948>
..@ phenoData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
.. .. ..@ varMetadata :'data.frame': 7 obs. of 1 variable:
.. .. .. ..$ labelDescription: chr [1:7] "hapmap family id" "hapmap person id" "id of mother of this person" "id of father of this person" ...
.. .. ..@ data :'data.frame': 90 obs. of 7 variables:
.. .. .. ..$ famid : int [1:90] 1341 1341 1341 1340 1340 1340 1340 1340 1341 1341 ...
.. .. .. ..$ persid : int [1:90] 14 2 13 9 10 2 11 1 11 1 ...
.. .. .. ..$ mothid : int [1:90] 0 14 0 0 0 12 0 10 0 12 ...
.. .. .. ..$ fathid : int [1:90] 0 13 0 0 0 11 0 9 0 11 ...
.. .. .. ..$ sampid : Factor w/ 90 levels "NA06985","NA06991",..: 1 2 3 4 5 6 7 8 9 10 ...
.. .. .. ..$ isFounder: logi [1:90] TRUE FALSE TRUE TRUE TRUE FALSE ...
.. .. .. ..$ male : logi [1:90] FALSE FALSE TRUE TRUE FALSE FALSE ...
.. .. ..@ dimLabels : chr [1:2] "sampleNames" "sampleColumns"
.. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots
.. .. .. .. ..@ .Data:List of 1
.. .. .. .. .. ..$ : int [1:3] 1 1 0
..@ featureData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
.. .. ..@ varMetadata :'data.frame': 0 obs. of 1 variable:
.. .. .. ..$ labelDescription: chr(0)
.. .. ..@ data :'data.frame': 47293 obs. of 0 variables
.. .. ..@ dimLabels : chr [1:2] "featureNames" "featureColumns"
.. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots
.. .. .. .. ..@ .Data:List of 1
.. .. .. .. .. ..$ : int [1:3] 1 1 0
..@ annotation : chr "illuminaHumanv1.db"
..@ protocolData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots
.. .. ..@ varMetadata :'data.frame': 0 obs. of 1 variable:
.. .. .. ..$ labelDescription: chr(0)
.. .. ..@ data :'data.frame': 90 obs. of 0 variables
.. .. ..@ dimLabels : chr [1:2] "sampleNames" "sampleColumns"
.. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots
.. .. .. .. ..@ .Data:List of 1
.. .. .. .. .. ..$ : int [1:3] 1 1 0
..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots
.. .. ..@ .Data:List of 4
.. .. .. ..$ : int [1:3] 2 14 0
.. .. .. ..$ : int [1:3] 2 13 7
.. .. .. ..$ : int [1:3] 1 3 0
.. .. .. ..$ : int [1:3] 1 0 0

Details

Expression data harvested in 2007 from GENEVAR

ftp://ftp.sanger.ac.uk/pub/genevar/CEU_parents_norm_march2007.zip

Examples

data(eset) # yields ExpressionSet instance called ex

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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'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(GGtools)
Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Loading required package: data.table
Loading required package: parallel
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

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:Matrix':

    colMeans, colSums, expand, rowMeans, rowSums

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

    colMeans, colSums, expand.grid, rowMeans, rowSums


Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene

Attaching package: 'GGtools'

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

    getCall

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GGtools/ex.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ex
> ### Title: ExpressionSet instance for illustrating integrative smlSet
> ###   container
> ### Aliases: ex
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(eset) # yields ExpressionSet instance called ex
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>