expSetSpeCondExample: An ExpressionSet example object used in the SpeCond package

In SpeCond: Condition specific detection from expression data

Description

expSetSpeCondExample is an ExpressionSet example object used as an example for the SpeCond package. This ExpressionSet only contains an expression matrix and the phenoData. This object has only the purpose of illustrating how SpeCond can be used with an ExpressionSet input object.

Usage

data(expSetSpeCondExample)

Format

The format is: Formal class 'ExpressionSet' [package "Biobase"] with 7 slots ..@ phenoData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 2 obs. of 1 variable: .. .. .. ..$ labelDescription: chr [1:2] "Tissue names" "Experience number" .. .. ..@ data :'data.frame': 64 obs. of 2 variables: .. .. .. ..$ Tissue: Factor w/ 32 levels "Adrenal_cortex",..: 23 23 5 5 1 1 16 16 32 32 ... .. .. .. .. ..- attr(*, "names")= chr [1:64] "S_1" "S_2" "S_3" "S_4" ... .. .. .. ..$ Exp : Factor w/ 2 levels "Exp1","Exp2": 1 2 1 2 1 2 1 2 1 2 ... .. .. .. .. ..- attr(*, "names")= chr [1:64] "S_1" "S_2" "S_3" "S_4" ... .. .. ..@ 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

Author(s)

Florence Cavalli, [e-mail]

See Also

getMatrixFromExpressionSet

Examples

data(expSetSpeCondExample)

Example output

Loading required package: mclust
Package 'mclust' version 5.4.3
Type 'citation("mclust")' for citing this R package in publications.
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: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.2-2 (2019-03-07) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

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

    backsolve, forwardsolve

Loading required package: maps

Attaching package: 'maps'

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

    map

See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 
Loading required package: hwriter
Loading required package: RColorBrewer

SpeCond documentation built on Nov. 8, 2020, 4:57 p.m.