R/readCdfGroupStrands.R

In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

readCdfGroupStrands <- function(..., what=c("probe", "target")) {
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  # Validate arguments
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  # Argument 'what':
  what <- match.arg(what)


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  # Read the strand information from the CDF file
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  cdf <- .readCdf(..., readUnitDirection=TRUE, readGroupDirection=TRUE,
         readXY=FALSE, readBases=FALSE, readIndexpos=FALSE, readIsPm=FALSE,
                                      readAtoms=FALSE, readUnitType=FALSE)

  getTarget <- (what == "target")


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  # Extract the strandinformation
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  swapIdxs <- c()
  for (uu in seq_along(cdf)) {
    unit <- .subset2(cdf, uu)

    unitDirection <- .subset2(unit, "unitdirection")
    strands <- unlist(.subset2(unit, "groups"), use.names=FALSE)
    if (identical(unitDirection, "antisense")) {
      strands <- c(sense="antisense", antisense="sense")[strands]
      swapIdxs <- c(swapIdxs, uu)
    }

    # Get strands for target?
    if (getTarget)
      strands <- c(sense="antisense", antisense="sense")[strands]
    strands <- unname(strands)

    cdf[[uu]] <- strands
  }

  attr(cdf, "swapIdxs") <- swapIdxs

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  # Return a list of character vector
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  cdf
}