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Last data update: 2014.03.03

R: Sample data set for tRanslatome

tRanslatomeSampleData

R Documentation

Sample data set for tRanslatome

Description

matrix with data coming from differentiated and undifferentiated human HepaRG cells

Usage

data(tRanslatomeSampleData)

Format

tRanslatomeSampleData is a list that has 7 components :

expressionMatrix is a matrix of 12 columns and 1000 rows containing the microarray signals used as input of the function GetDEGs. Columns are organized in biological triplicates as follows: tot.diff.a, tot.diff.b, tot.diff.c contain the signals coming from the transcriptome of the differentiated cell line.

tot.undiff.a, tot.undiff.b, tot.undiff.c contain the signals coming from the transcriptome of the undifferentiated cell line.

pol.diff.a, pol.diff.b, pol.diff.c contain the signals coming from the translatome of the differentiated cell line.

pol.undiff.a, pol.undiff.b, pol.undiff.c contain the signals coming from the translatome of the undifferentiated cell line.

translatome.analysis is an object of class TranslatomeDataset generated calling newTranslatomeDataset() on expressionMatrix (see the examples section for the exactcall).

limma.DEGs is an object of class DEGs generated calling getDEGs() on expressionMatrix (see the examples section for the exact call).

CCEnrichment is an object of class GOsets generated calling GOEnrichment() on limma.DEGs (see the examples section for the exact call).

CCComparison is an object of class GOsims generated calling GOComparison() on CCEnrichment (see the examples section for the exact call).

regulatory.elements.counts is an object of class data.frame containing the background numbers of regulated and non-regulated genes for each post-transcriptional regulatory factor considered by function RegulatoryEnrichment.

regulatory.elements.regulated is an object of class data.frame containing the list of regulated genes for each post-transcriptional regulatory factor considered by function RegulatoryEnrichment

Source

Parent R, Kolippakkam D, Booth G, Beretta L. Mammalian target of rapamycin activation impairs hepatocytic differentiation and targets genes moderating lipid homeostasis and hepatocellular growth. Cancer Res. 2007;67(9):4337-4345

Examples

 ##load the tRanslatome sample data
 data(tRanslatomeSampleData)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(tRanslatome)
Loading required package: limma
Loading required package: sigPathway
Loading required package: samr
Loading required package: impute
Loading required package: matrixStats
matrixStats v0.50.2 (2016-04-24) successfully loaded. See ?matrixStats for help.
Loading required package: anota
Loading required package: qvalue
Loading required package: DESeq
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 object is masked from 'package:limma':

    plotMA

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")'.


Attaching package: 'Biobase'

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

    anyMissing, rowMedians

Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.
Loading required package: edgeR
Loading required package: RankProd
Loading required package: topGO
Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
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: SparseM

Attaching package: 'SparseM'

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

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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

    members

Loading required package: org.Hs.eg.db

Loading required package: GOSemSim
Loading required package: Heatplus
Loading required package: gplots

Attaching package: 'gplots'

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

    space

The following object is masked from 'package:S4Vectors':

    space

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

    lowess

Loading required package: plotrix

Attaching package: 'plotrix'

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

    plotCI

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/tRanslatome/tRanslatomeSampleData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: tRanslatomeSampleData
> ### Title: Sample data set for tRanslatome
> ### Aliases: tRanslatomeSampleData translatome.analysis CCEnrichment
> ###   limma.DEGs tRanslatomeData expressionMatrix CCComparison
> ###   regulatory.elements.counts regulatory.elements.regulated
> ### Keywords: datasets
> 
> ### ** Examples
> 
>  ##load the tRanslatome sample data
>  data(tRanslatomeSampleData) 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>