R/AffymetrixTsvFile.R

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

# @author "HB"
setConstructorS3("AffymetrixTsvFile", function(...) {
  this <- extend(AffymetrixFile(...), "AffymetrixTsvFile",
    "cached:.cdf" = NULL,
    "cached:.data" = NULL
  )
  if (isFile(this)) verify(this)
  this
})

setMethodS3("getChipType", "AffymetrixTsvFile", function(this, ...) {
  getName(this)
})

setMethodS3("getDefaultExtension", "AffymetrixTsvFile", function(static, ...) {
  "tsv"
}, static=TRUE, protected=TRUE)

setMethodS3("getExtensionPattern", "AffymetrixTsvFile", function(static, ...) {
  ext <- getDefaultExtension(static, ...)
  pattern <- sprintf("[.](%s|%s)$", tolower(ext), toupper(ext))
  pattern
}, static=TRUE, protected=TRUE)


setMethodS3("findByChipType", "AffymetrixTsvFile", function(static, chipType, ...) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Search in annotationData/chipTypes/<chipType>/
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  pattern <- sprintf("^%s%s", chipType, getExtensionPattern(static))
  pathname <- findAnnotationDataByChipType(chipType, pattern)

  pathname
}, static=TRUE, protected=TRUE)


setMethodS3("byChipType", "AffymetrixTsvFile", function(static, chipType, ...) {
  # Search for the genome information file
  pathname <- findByChipType(static, chipType, ...)
  if (is.null(pathname))
    throw("Failed to located Affymetrix TSV file: ", chipType)
  newInstance(static, pathname)
})

setMethodS3("verify", "AffymetrixTsvFile", function(this, ...) {
  tryCatch({
    df <- readDataFrame(this, nrows=10)
  }, error = function(ex) {
    throw("File format error of the Affymetrix TSV file: ",
                                                  getPathname(this))
  })
  invisible(TRUE)
}, private=TRUE)

setMethodS3("getData", "AffymetrixTsvFile", function(this, force=FALSE, ...) {
  data <- this$.data
  if (force || is.null(data)) {
    data <- readDataFrame(this, ...)
    this$.data <- data
  }
  data
})

setMethodS3("readDataFrame", "AffymetrixTsvFile", function(this, ..., verbose=FALSE) {
  pathname <- getPathname(this)

  colClasses <- c(
    "probeset_id"="character",
    "chr"="character",
    "snp_pos"="integer",
    "len"="integer",
    "GC"="double",
    "gc_count"="integer"
  )

  df <- readTable(pathname, colClasses=colClasses, header=TRUE, sep="\t", ...)

  names <- colnames(df)
  names <- gsub("probeset_id", "unit", names)
  names <- gsub("chr", "chromosome", names)
  names <- gsub("GC", "gc", names)
  names <- gsub("snp_pos", "physical position", names)
  names <- gsub("_", " ", names)
  names <- toCamelCase(names)
  colnames(df) <- names

  # Rescale GC contents to [0,1]
  df[["gc"]] <- df[["gc"]]/100

  # Remap chromsome X->23, Y->24
  chr <- df[["chromosome"]]
  chr[chr == "X"] <- 23
  chr[chr == "Y"] <- 24
  suppressWarnings({
    chr <- as.integer(chr)
  })
  df[["chromosome"]] <- chr
  # Not needed anymore
  chr <- NULL

  # Remove duplicated rows (type by Affymetrix?!? /HB 2007-04-02)
  df <- unique(df)

  gc()

  # Convert unit names to unit indices
  unf <- getUnitNamesFile(this)
  unitNames <- getUnitNames(unf)
  units <- match(df[["unit"]], unitNames)
  if (any(is.na(units))) {
    throw("File format error: Identified units that do not exist in the annotation unit names file: ", getChipType(unf))
  }
  df[["unit"]] <- units

#  rownames(df) <-  units

  o <- order(units)
  df <- df[o,]

  df
})


setMethodS3("getField", "AffymetrixTsvFile", function(this, units=NULL, field, ...) {
  if (is.null(units)) {
    unf <- getUnitNamesFile(this)
    units <- seq_len(nbrOfUnits(unf))
  }

  data <- getData(this, ...)
  if (!field %in% colnames(data))
    throw("No such field: ", field)

  idxs <- match(units, data$unit)
  data[[field]][idxs]
})

setMethodS3("getPosition", "AffymetrixTsvFile", function(this, ...) {
  getField(this, field="physicalPosition", ...)
})

setMethodS3("getFragmentLengths", "AffymetrixTsvFile", function(this, ...) {
  getField(this, field="len", ...)
})

setMethodS3("getGc", "AffymetrixTsvFile", function(this, ...) {
  getField(this, field="gc", ...)
})



# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# BEGIN: Methods that requires an Affymetrix CDF file
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
setMethodS3("getCdf", "AffymetrixTsvFile", function(this, ...) {
  cdf <- this$.cdf
  if (is.null(cdf)) {
    chipType <- getChipType(this)
    cdf <- AffymetrixCdfFile$byChipType(chipType)
    this$.cdf <- cdf
  }
  cdf
})

# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# END: Methods that requires an Affymetrix CDF file
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -