Test data of miRNA and mRNA expression vector.

Description

Test data of miRNA and mRNA expression vector from the same human individial that is used in the vignette.

Usage

data(tcga_gbm_testdata)

Format

A data frame with 11884 mRNA expression and 373 miRNA expression on the following 2 variables.

x

a numeric vector for expression of 11884 mRNAs

y

a numeric vector for expression of 373 miRNA

Details

The miRNA and mRNA expression data for the same individual (barcode ID: TCGA-02-0001-01) were downloaded from TCGA (The Cancer Genome Altas) GBM (Glioblastoma multiforme). To eliminate negative values in the expression matrices, we linearly transformed all of the data to positive scale with range between 0 and the maximum of the positive values using rescale R function. The resulting data were further processed by filtering out miRNAs or mRNAs without any seed/seed match based on the Microcosm database. As a result, the test data contain the expression for 11884 distinct mRNA and distinct 373 miRNA.

Source

https://tcga-data.nci.nih.gov

References

Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic acids research 36: D154-8

Examples

data(tcga_gbm_testdata)

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 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(Roleswitch)
Loading required package: pracma
Loading required package: reshape
Loading required package: plotrix
Loading required package: microRNA
Loading required package: biomaRt
Loading required package: Biostrings
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand, rename

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
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: DBI
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Roleswitch/tcga_gbm_testdata.Rd_%03d_medium.png", width=480, height=480)
> ### Name: tcga_gbm_testdata
> ### Title: Test data of miRNA and mRNA expression vector.
> ### Aliases: tcga_gbm_testdata
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(tcga_gbm_testdata)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>