converts a Ringo MAList into an ExpressionSet

Description

Function to convert an object of class MAList into an object of class ExpressionSet. Note that the otherwise optional targets component is required in this case to generate the phenoData of the new ExpressionSet.

Usage

asExprSet(from, idColumn="PROBE_ID")

Arguments

Value

an object of class ExpressionSet

Note

There is a more general function for converting MALists to ExpressionSets in the package convert. This function here is solely intended for converting Ringo-generated MALists into ExpressionSets.

Author(s)

Joern Toedling

See Also

ExpressionSet, preprocess

Examples

  exDir <- system.file("exData",package="Ringo")
  exRG  <- readNimblegen("example_targets.txt","spottypes.txt",path=exDir)
  exMA  <- preprocess(exRG, "none", returnMAList=TRUE)
  exX   <- asExprSet(exMA)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(Ringo)
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, 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")'.

Loading required package: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: Matrix
Loading required package: grid
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Ringo/asExprSet.Rd_%03d_medium.png", width=480, height=480)
> ### Name: asExprSet
> ### Title: converts a Ringo MAList into an ExpressionSet
> ### Aliases: asExprSet asExpressionSet
> ### Keywords: manip
> 
> ### ** Examples
> 
>   exDir <- system.file("exData",package="Ringo")
>   exRG  <- readNimblegen("example_targets.txt","spottypes.txt",path=exDir)
Reading targets file...
Reading raw intensities...
Read header information
Read /home/ddbj/local/lib64/R/library/Ringo/exData/MOD_20551_PMT1_pair.txt 
Read /home/ddbj/local/lib64/R/library/Ringo/exData/MOD_20742_PMT1_pair.txt 
Determining probe categories...
Matching patterns for: GENE_EXPR_OPTION PROBE_ID 
Found 991 Probe 
Found 0 Probe 
Found 0 Probe 
Found 0 Negative 
Found 0 Empty 
Found 0 H_Code 
Found 0 V_Code 
Found 0 Random 
Setting attributes: values Color 
>   exMA  <- preprocess(exRG, "none", returnMAList=TRUE)
Normalizing...
>   exX   <- asExprSet(exMA)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>