Convert data from RTCGA family to Bioconductor classes

Description

Functions use Biobase (http://bioconductor.org/packages/release/bioc/html/Biobase.html) package to transform data from packages from RTCGA data family to Bioconductor classes (RTCGA.rnaseq, RTCGA.RPPA, RTCGA.PANCAN12, mRNA, RTCGA.methylation to ExpressionSet and RTCGA.CNV to GRanges). For RTCGA.PANCAN12 there is sense to convert expression.cb1, expression.cb2, cnv.cb.

Usage

convertTCGA(dataSet, dataType = "expression")

convertPANCAN12(dataSet)

Arguments

Details

This functionality is motivated by that we were asked to offer the data in Bioconductor-friendly classes because many users already have their data in one of the core infrastructure classes. Data of the same type in compatible containers promotes interoperability and makes it easy to combine and organize.

Bioconductor classes were designed to capitalize on the biological structure of the data. If data have a range-based component it's natural, for Bioconductor users, to store and access these as a GRanges where they can extract position, strand etc. in the same way. Similarly for ExpressionSet. This class holds expression data along with experiment metadata and comes with built in accessors to extract and manipulate data. The idea is to offer a common API to the data; extracting the start position in a GRanges is always start(). With a data.frame it is different each time (unless select() is implemented) as the column names and organization of data can be different.

AnnotationHub and the soon to come ExperimentHub will host many different types of data. A primary goal moving forward is to offer similar data in a consistent format. For example, CNV data in AnnotationHub is offered as a GRanges and as more CNV are added we will ask that they too are packaged as GRanges. The aim is that streamlined data on the back-end will make for a more intuitive experience on the front-end.

Value

Functions return an ExpressionSet or a GRanges for RTCGA.CNV

Biobase and GenomicRanges

This function use tools from the fantastic Biobase (and GenomicRanges for CNV) package, so you'll need to make sure to have it installed.

Issues

If you have any problems, issues or think that something is missing or is not clear please post an issue on https://github.com/RTCGA/RTCGA/issues.

Author(s)

Marcin Kosinski, m.p.kosinski@gmail.com

See Also

RTCGA website http://rtcga.github.io/RTCGA/Download.html.

Other RTCGA: RTCGA-package, boxplotTCGA, checkTCGA, datasetsTCGA, downloadTCGA, expressionsTCGA, heatmapTCGA, infoTCGA, installTCGA, kmTCGA, mutationsTCGA, pcaTCGA, readTCGA, survivalTCGA, theme_RTCGA

Examples

########
########
# Expression data
########
########
library(RTCGA.rnaseq)
library(Biobase)
convertTCGA(BRCA.rnaseq) -> BRCA.rnaseq_ExpressionSet
## Not run: 
library(RTCGA.PANCAN12)
convertPANCAN12(expression.cb1) -> PANCAN12_ExpressionSet
library(RTCGA.RPPA)
convertTCGA(BRCA.RPPA) -> BRCA.RPPA_ExpressionSet
library(RTCGA.methylation)
convertTCGA(BRCA.methylation) -> BRCA.methylation_ExpressionSet
library(RTCGA.mRNA)
convertTCGA(BRCA.mRNA) -> BRCA.mRNA_ExpressionSet 
########
########
# CNV
########
########
library(RTCGA.CNV)
library(GRanges)
convertTCGA(BRCA.CNV, "CNV") -> BRCA.CNV_GRanges


## End(Not run)

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.
Type 'q()' to quit R.

> library(RTCGA)
Welcome to the RTCGA (version: 1.2.2).
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RTCGA/convertTCGA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: convertTCGA
> ### Title: Convert data from RTCGA family to Bioconductor classes
> ### Aliases: convertPANCAN12 convertTCGA
> 
> ### ** Examples
> 
> 
> 
> ########
> ########
> # Expression data
> ########
> ########
> library(RTCGA.rnaseq)
> library(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, 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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> convertTCGA(BRCA.rnaseq) -> BRCA.rnaseq_ExpressionSet
> ## Not run: 
> ##D library(RTCGA.PANCAN12)
> ##D convertPANCAN12(expression.cb1) -> PANCAN12_ExpressionSet
> ##D library(RTCGA.RPPA)
> ##D convertTCGA(BRCA.RPPA) -> BRCA.RPPA_ExpressionSet
> ##D library(RTCGA.methylation)
> ##D convertTCGA(BRCA.methylation) -> BRCA.methylation_ExpressionSet
> ##D library(RTCGA.mRNA)
> ##D convertTCGA(BRCA.mRNA) -> BRCA.mRNA_ExpressionSet 
> ##D ########
> ##D ########
> ##D # CNV
> ##D ########
> ##D ########
> ##D library(RTCGA.CNV)
> ##D library(GRanges)
> ##D convertTCGA(BRCA.CNV, "CNV") -> BRCA.CNV_GRanges
> ##D 
> ## End(Not run)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>