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  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2014-06-08 14:24:15 UTC
  • mfrom: (1.1.1)
  • Revision ID: package-import@ubuntu.com-20140608142415-cdpkgnsvgan8qhzr
Tags: 1.42.2-1
* New upstream version
* Add citation
* Add autopkgtest

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R/read.affybatch.R
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## Dec 12, 2006 - added checkCelFiles() to ensure all filenames are celfiles so unintended
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##                arguments don't get passed in via ...
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## Apr 19, 2013 - JWM: added warning and error messages for Gene ST and Exon ST arrays
 
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## Sept 26, 2013 - naked .Call() to affyio replaced
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##
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#############################################################
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      warning(paste0("\n\nThe affy package can process data from the Gene ST 1.x series of arrays,\n",
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                    "but you should consider using either the oligo or xps packages, which are specifically\n",
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                     "designed for these arrays.\n\n"), call. = FALSE)
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  if(length(grep("gene2[01]st|ex[1-2][0-1]st", cleancdfname(ref.cdfName))) == 1)
 
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  if(length(grep("gene2[01]st|ex[1-2][0-1]st|hta20", cleancdfname(ref.cdfName))) == 1)
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      stop(paste0("\n\nThe affy package is not designed for this array type.\n",
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                   "Please use either the oligo or xps package.\n\n"), .call = FALSE)
 
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                   "Please use either the oligo or xps package.\n\n"), call. = FALSE)
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  scandates <-
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  ## Change sampleNames to be consistent with row.names of phenoData
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  ## object
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  exprs <- .Call("read_abatch",filenames, rm.mask,
 
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  exprs <-  affyio::read_abatch(filenames, rm.mask,
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               rm.outliers, rm.extra, ref.cdfName,
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               dim.intensity[c(1,2)],verbose, PACKAGE="affyio")
 
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               dim.intensity[c(1,2)],verbose)
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  colnames(exprs) <- samplenames
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  #### this is where the code changes from the original read.affybatch.
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  } else {
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    return(new("AffyBatch",
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               exprs  = exprs,
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               se.exprs = .Call("read_abatch_stddev",filenames, rm.mask,
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                 rm.outliers, rm.extra, ref.cdfName,
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                 dim.intensity,verbose, PACKAGE="affyio"),
 
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               se.exprs =  affyio::read_abatch_stddev(filenames, rm.mask,
 
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               rm.outliers, rm.extra, ref.cdfName,
 
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               dim.intensity[c(1,2)],verbose),
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               cdfName    = cdfname,   ##cel@cdfName,
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               phenoData  = phenoData,
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               nrow       = dim.intensity[2],##["Rows"],
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    }
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  }
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  chkSn <- function(filenames, samplenames){
 
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      fntest <- sub("^/?([^/]*/)*", "", filenames)
 
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      if(all(fntest %in% samplenames)){
 
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          filenames <<- filenames[match(samplenames, fntest)]
 
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      } else {
 
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          warning(paste0("Mismatched phenoData and celfile names!\n\n",
 
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                         "Please note that the row.names of your phenoData ",
 
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                         "object should be identical to what you get from ",
 
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                         "list.celfiles()!\nOtherwise you are responsible for ",
 
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                         "ensuring that the ordering of your phenoData object ",
 
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                         "conforms to the ordering of the celfiles as they are ",
 
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                         "read into the AffyBatch!\nIf not, errors may ",
 
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                         "result from using the phenoData for subsetting or ",
 
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                         "creating linear models, etc.\n\n"),
 
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                  call. = FALSE)
 
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      }
 
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  }
 
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  if(is.character(phenoData)) { 
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    ## if character, read file 
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    if(length(phenoData)!=1) stop(sprintf("'phenoData' must be of length 1, but is %d.", length(phenoData)))
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    phenoData <- read.AnnotatedDataFrame(filename=phenoData)
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    sampleNames <- sampleNames(phenoData)
 
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    chkSn(filenames, sampleNames)
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  } else if(is.data.frame(phenoData)) {
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    ## if data.frame, coerce
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    phenoData <-  as(phenoData, "AnnotatedDataFrame")
 
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    sampleNames <- sampleNames(phenoData)
 
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    chkSn(filenames, sampleNames)
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  } else if(is.null(phenoData)) {
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    phenoData <- new("AnnotatedDataFrame",
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                     data = data.frame(sample=seq_along(sampleNames),