R/DChipSnpInformation.R

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

###########################################################################/**
# @RdocClass DChipSnpInformation
#
# @title "The DChipSnpInformation class"
#
# \description{
#  @classhierarchy
#
#  This class represents dChip genome information files, which typically
#  contains information on nucleotide sequences and fragment lengths
#  of the units.
# }
#
# @synopsis
#
# \arguments{
#   \item{...}{Arguments passed to @see "SnpInformation".}
# }
#
# \section{Fields and Methods}{
#  @allmethods "public"
# }
#
# \details{
#   The dChip SNP information files for various chip types can be
#   downloaded from \url{https://sites.google.com/site/dchipsoft/}.
#   Put each file in a
#   directory named identically as the corresponding chip type under the
#   \emph{annotations/} directory, e.g.
#   \emph{annotations/Mapping50K_Hind240/50k hind snp info AfAm
#   june 05 hg17.xls}.
#   Note that dChip changes the filename and file format slightly between
#   chip types, but currently the @seemethod "byChipType" basically searches
#   for files with names consisting of \code{"snp info"} or
#   \code{"snp_info"}.  At least for the most common chip types, there
#   is no need to rename the files in order for this class to recognize them.
# }
#
# @author "HB"
#*/###########################################################################
setConstructorS3("DChipSnpInformation", function(...) {
  this <- extend(SnpInformation(...), "DChipSnpInformation")
  if (isFile(this)) verify(this)
  this
})



setMethodS3("findByChipType", "DChipSnpInformation", function(static, chipType, version=NULL, ...) {
  # Argument 'version':
  if (is.null(version))
    version <- ".*"

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Search in annotationData/chipTypes/<chipType>/
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  pattern <- sprintf("^.*( |_)snp( |_)info(| |_).*%s[.](txt|xls)$", version)
  pathname <- findAnnotationDataByChipType(chipType, pattern)


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # As a backup search the "old" style
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  if (is.null(pathname)) {
    path <- filePath("annotations", chipType)
    path <- Arguments$getReadablePath(path, mustExist=FALSE)

    if (isDirectory(path)) {
      pathnames <- list.files(path=path, pattern=pattern, full.names=TRUE)
      nfiles <- length(pathnames)
      if (nfiles > 1) {
        pathnames <- sort(pathnames)
        warning("Found more than one matching dChip genome information file, but returning only the last one: ", paste(pathnames, collapse=", "))
        pathnames <- rev(pathnames)
        pathname <- pathnames[1]
      }
    }
  }

  pathname
}, static=TRUE, protected=TRUE)


###########################################################################/**
# @RdocMethod byChipType
#
# @title "Defines a DChipSnpInformation object by chip type"
#
# \description{
#  @get "title".
# }
#
# @synopsis
#
# \arguments{
#  \item{chipType}{A @character string.}
#  \item{version}{An optional @character string specifying the version
#    string, if more than one version is available.}
#  \item{...}{Additional arguments passed to @seemethod "findByChipType".}
# }
#
# \value{
#  Returns an @see "DChipSnpInformation" object.
#  If no file was not found, an error is thrown.
# }
#
# \seealso{
#   @seeclass
# }
#
# @keyword IO
# @keyword programming
#*/###########################################################################
setMethodS3("byChipType", "DChipSnpInformation", function(static, chipType, version=NULL, ...) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }

  verbose && enter(verbose, "Defining ", class(static)[1], " from chip type")
  verbose && cat(verbose, "Chip type: ", chipType)
  verbose && cat(verbose, "Version: ", version)

  # Search for the genome information file
  pathname <- findByChipType(static, chipType, version=version, ..., verbose=verbose)
  verbose && cat(verbose, "Located pathname: ", pathname)

  if (is.null(pathname))
    throw("Failed to located dChip genome information: ", chipType)

  verbose && enter(verbose, "Instantiating ", class(static)[1])
  res <- newInstance(static, pathname)
  verbose && print(verbose, res)
  verbose && exit(verbose)

  verbose && exit(verbose)

  res
})


setMethodS3("verify", "DChipSnpInformation", function(this, ...) {
  tryCatch({
    df <- readDataFrame(this, nrow=10)
  }, error = function(ex) {
    throw("File format error of the dChip SNP information file (",
                                 ex$message, "): ", getPathname(this))
  })
  invisible(TRUE)
}, private=TRUE)


setMethodS3("readDataFrame", "DChipSnpInformation", function(this, ...) {
  readFcns <- list(
    "^Mapping10K" = read10K,
    "^Mapping50K" = read50K,
    "^Mapping250K" = read250K
  )

  chipType <- getChipType(this)

  # Try to read with the designated read function.
  res <- NULL
  for (kk in seq_along(readFcns)) {
    pattern <- names(readFcns)[kk]
    if (regexpr(pattern, chipType) != -1) {
      readFcn <- readFcns[[kk]]
      tryCatch({
        res <- readFcn(this, ...)
      }, error=function(ex) {})
    }
  }

  # If failed, re-try using all read functions.
  if (is.null(res)) {
    for (kk in seq_along(readFcns)) {
      readFcn <- readFcns[[kk]]
      tryCatch({
        res <- readFcn(this, ...)
      }, error=function(ex) {})
      if (!is.null(res))
        break
    }
  }

  if (is.null(res)) {
    throw("Cannot read dChip SNP information file.  No predefined read function available for this chip type: ", chipType)
  }

  res
})




setMethodS3("read250K", "DChipSnpInformation", function(this, ..., exclude=c("dbSNP RS ID", "Flank", "FreqAsia", "FreqAfAm", "FreqCauc")) {
  # Example with TABs replaced by semicolons:
  # Probe Set ID;dbSNP RS ID;Flank;Fragment Length Start Stop;FreqAsia;FreqAfAm;FreqCauc
  # SNP_A-1780520;rs16994928;ggatagtgttgacctc[A/G]agtacaggtttcaaaa;496 // 47873735 // 47874230;0.0 ;0.11;0.0
  colClasses <- c(
    "Probe Set ID"="character",
    "dbSNP RS ID"="character",
    "Flank"="character",
    "Fragment Length Start Stop"="character",
    "FreqAsia"="double",
    "FreqAfAm"="double",
    "FreqCauc"="double"
  )
  readTableInternal(this, pathname=getPathname(this), colClasses=colClasses, exclude=exclude, ...)
}, private=TRUE)

setMethodS3("read50K", "DChipSnpInformation", function(this, ..., exclude=c("dbSNP RS ID", "Flank", "FreqAsian", "FreqAfAm", "FreqCauc")) {
  colClasses <- c(
    "Probe Set ID"="character",
    "dbSNP RS ID"="character",
    "Flank"="character",
    "Fragment Length Start Stop"="character",
    "FreqAsian"="double",
    "FreqAfAm"="double",
    "FreqCauc"="double"
  )
  readTableInternal(this, pathname=getPathname(this), colClasses=colClasses, exclude=exclude, ...)
}, private=TRUE)

setMethodS3("read10K", "DChipSnpInformation", function(this, ..., exclude=c("dbSNP RS ID", "Flank", "Freq Asian", "Freq AfAm", "Freq Cauc"), fill=TRUE) {
  colClasses <- c(
    "Probe Set ID"="character",
    "dbSNP RS ID"="character",
    "Flank"="character",
    "Fragment Length Start Stop"="character",
    "Freq Asian"="double",
    "Freq AfAm"="double",
    "Freq Cauc"="double"
  )
  readTableInternal(this, pathname=getPathname(this), colClasses=colClasses, exclude=exclude, fill=fill, ...)
}, private=TRUE)