Return a data.frame of AssayData name substitutions.

Description

The Illumina methylation platforms use two distinct platforms, the "goldengate" platform and the "infinium" platform. Each of these uses different file formats as well as different assay techologies. To make the downstream data handling more straightforward and uniform between the two different systems, a simple mapping from the column names in the output files from the Illumina software is used to convert things from Red/Green or Cy5/Cy3 to unmethylated/methylated. This function simply returns that mapping.

Usage

getAssayDataNameSubstitutions()

Details

A file in the extdata directory called "substitutions.txt" contains two columns. The function loads this file and uses the first column as a match against column names in the data file (with the "sample part" removed). If matched, the second column gives the replacement.

Value

A data.frame with two columns, regex and replacement.

Author(s)

Sean Davis <seandavi@gmail.com>

Examples

getAssayDataNameSubstitutions()

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 'contributors()' for more information and
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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(methylumi)
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':

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

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    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")'.

Loading required package: scales
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Loading required package: ggplot2
Loading required package: matrixStats
matrixStats v0.50.2 (2016-04-24) successfully loaded. See ?matrixStats for help.

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: FDb.InfiniumMethylation.hg19
Loading required package: GenomicFeatures
Loading required package: S4Vectors
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Attaching package: 'S4Vectors'

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    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
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Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Loading required package: org.Hs.eg.db

Loading required package: minfi
Loading required package: lattice
Loading required package: SummarizedExperiment

Attaching package: 'SummarizedExperiment'

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

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Loading required package: Biostrings
Loading required package: XVector
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Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/methylumi/getAssayDataNameSubstitutions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getAssayDataNameSubstitutions
> ### Title: Return a data.frame of AssayData name substitutions.
> ### Aliases: getAssayDataNameSubstitutions
> ### Keywords: IO
> 
> ### ** Examples
> 
> getAssayDataNameSubstitutions()
           regex       result
1       AVG_Beta        betas
2 Detection Pval        pvals
3     Signal CY3 unmethylated
4     Signal CY5   methylated
5     Signal_Red unmethylated
6     Signal_Grn   methylated
7       Signal_A unmethylated
8       Signal_B   methylated
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>