WIGFile-class: WIG Import and Export
In rtracklayer: R interface to genome annotation files and the UCSC genome browser

Description Usage Arguments Details Value WIGFile objects Author(s) References Examples

These functions support the import and export of the UCSC WIG (Wiggle) format.

## S4 method for signature 'WIGFile,ANY,ANY'
import(con, format, text, genome = NA,
                    trackLine = TRUE, which = NULL, seqinfo = NULL, ...)
import.wig(con, ...)

## S4 method for signature 'ANY,WIGFile,ANY'
export(object, con, format, ...)
## S4 method for signature 'GenomicRanges,WIGFile,ANY'
export(object, con, format,
                   dataFormat = c("auto", "variableStep", "fixedStep"),
                   writer = .wigWriter, append = FALSE, ...)
## S4 method for signature 'GenomicRangesList,WIGFile,ANY'
export(object, con, format, ...)
## S4 method for signature 'UCSCData,WIGFile,ANY'
export(object, con, format,
                   trackLine = TRUE, ...)
export.wig(object, con, ...)

`con`	A path, URL, connection or `WIGFile` object. For the functions ending in `.wig`, the file format is indicated by the function name. For the base `export` and `import` functions, the format must be indicated another way. If `con` is a path, URL or connection, either the file extension or the `format` argument needs to be “wig”. Compressed files (“gz”, “bz2” and “xz”) are handled transparently.
`object`	The object to export, should be a `GRanges` or something coercible to a `GRanges`. For exporting multiple tracks, in the UCSC track line metaformat, pass a `GenomicRangesList`, or something coercible to one.
`format`	If not missing, should be “wig”.
`text`	If `con` is missing, a character vector to use as the input
`trackLine`	Whether to parse/output a UCSC track line. An imported track line will be stored in a `TrackLine` object, as part of the returned `UCSCData`.
`genome`	The identifier of a genome, or `NA` if unknown. Typically, this is a UCSC identifier like “hg19”. An attempt will be made to derive the `seqinfo` on the return value using either an installed BSgenome package or UCSC, if network access is available.
`seqinfo`	If not `NULL`, the `Seqinfo` object to set on the result. If the `genome` argument is not `NA`, it must agree with `genome(seqinfo)`.
`which`	A range data structure like `IntegerRangesList` or `GRanges`. Only the intervals in the file overlapping the given ranges are returned. This is inefficient; use BigWig for efficient spatial queries.
`append`	If `TRUE`, and `con` points to a file path, the data is appended to the file. Obviously, if `con` is a connection, the data is always appended.
`dataFormat`	Probably best left to “auto”. Exists only for historical reasons.
`writer`	Function for writing out the blocks; for internal use only.
`...`	Arguments to pass down to methods to other methods. For import, the flow eventually reaches the `WIGFile` method on `import`. When `trackLine` is `TRUE`, the arguments are passed through `export.ucsc`, so track line parameters are supported.

The WIG format is a text-based format for efficiently representing a dense genome-scale score vector. It encodes, for each feature, a range and score. Features from the same sequence (chromosome) are grouped together into a block, with a single block header line indicating the chromosome. There are two block formats: fixed step and variable step. For fixed step, the number of positions (or step) between intervals is the same across an entire block. For variable step, the start position is specified for each feature. For both fixed and variable step, the span (or width) is specified in the header and thus must be the same across all features. This requirement of uniform width dramatically limits the applicability of WIG. For scored features of variable width, consider BEDGraph or BigWig, which is generally preferred over both WIG and BEDGraph. To efficiently convert an existing WIG or BEDGraph file to BigWig, call wigToBigWig. Neither WIG, BEDGraph nor BigWig allow overlapping features.

A GRanges with the score values in the score metadata column, which is accessible via the score function.

The WIGFile class extends RTLFile and is a formal represention of a resource in the WIG format. To cast a path, URL or connection to a WIGFile, pass it to the WIGFile constructor.

Michael Lawrence

http://genome.ucsc.edu/goldenPath/help/wiggle.html

  test_path <- system.file("tests", package = "rtracklayer")
  test_wig <- file.path(test_path, "step.wig")

  ## basic import calls
  test <- import(test_wig)
  test
  import.wig(test_wig)
  test_wig_file <- WIGFile(test_wig)
  import(test_wig_file)
  test_wig_con <- file(test_wig)
  import(test_wig_con, format = "wig")
  test_wig_con <- file(test_wig)
  import(WIGFile(test_wig_con))

  ## various options
  import(test_wig, genome = "hg19")
  import(test_wig, trackLine = FALSE)
  which <- as(test[3:4,], "IntegerRangesList")
  import(test_wig, which = which)

## Not run: 
  ## basic export calls
  test_wig_out <- file.path(tempdir(), "test.wig")
  export(test, test_wig_out)
  export.wig(test, test_wig_out)
  test_foo_out <- file.path(tempdir(), "test.foo")
  export(test, test_foo_out, format = "wig")
  test_wig_out_file <- WIGFile(test_wig_out)
  export(test, test_wig_out_file)

  ## appending
  test2 <- test
  metadata(test2)$trackLine <- initialize(metadata(test)$trackLine,
                                          name = "test2")
  export(test2, test_wig_out_file, append = TRUE)

  ## passing track line parameters
  export(test, test_wig_out, name = "test2")

  ## no track line
  export(test, test_wig_out, trackLine = FALSE)
  
  ## gzip
  test_wig_gz <- paste(test_wig_out, ".gz", sep = "")
  export(test, test_wig_gz)

## End(Not run)