UCSCData-class {rtracklayer} | R Documentation

## Class "UCSCData"

### Description

Each track in UCSC has an associated `TrackLine` that contains metadata on the track.

### Slots

`trackLine`:

  Object of class `"TrackLine"` holding track metadata.

### Methods

`export.bed(object, con, variant = c("base", "bedGraph", "bed15"), color, trackLine = TRUE, ...)`

  Exports the track and its track line (if `trackLine` is `TRUE`) to `con` in the Browser Extended Display (BED) format. The arguments in `...` are passed to `export.ucsc`.

`export.bed15(object, con, expNames = NULL, ...)`

  Exports the track and its track line (if `trackLine` is `TRUE`) to `con` in the Bed15 format. The data is taken from the columns named in `expNames`, which defaults to the `expNames` in the track line, if any, otherwise all column names. The arguments in `...` are passed to `export.ucsc`.

`export.gff(object)`

  Exports the track and its track line (as a comment) to `con` in the General Feature Format (GFF).

`export.ucsc(object, con, subformat, ...)`

  Exports the track and its track line to `con` in the UCSC meta-format.

`as(object, "UCSCData")`

  Constructs a `UCSCData` from a `GRanges` instance, by adding a default track line and ensuring that the sequence/chromosome names are compliant with UCSC conventions. If there is a numeric score, the track line type is either "bedGraph" or "wig", depending on the feature density. Otherwise, "bed" is chosen.

### Author(s)

Michael Lawrence

### See Also

`import` and `export` for reading and writing tracks to and from connections (files), respectively.

[Package rtracklayer version 1.48.0 Index]