Rgb (version 1.5.1)

crossable-class: Class

Description

Reference classes extending this virtual class must have a slice method, as a generic cross method based on it is provided. Its only purpose is currently to add the cross method to "", as "" does not guarantee that slice returns a data.frame as crossable needs one.

Arguments

Extends

Class , directly. Class , by class , distance 2. All reference classes extend and inherit methods from .

Fields

The following fields are inherited (from the corresponding class):
  • name ()
  • parameters ()

Methods

cross(annotation, colname = , type = , fuzziness = , maxElements = , location = , precision = , quiet = ):
Add a new column computed from overlaps with an other crossable object. - annotation : other crossable object to compute overlap with. - colname : single character value, the name of the new column to add to .self. If NULL or NA, the result will be returned rather than added to .self. - type : single character value, either : 'cover', to compute coverage of 'annotation' elements for each .self element 'count', to count 'annotation' elements overlapping each .self element 'cytoband', to get cytogenetic coordinates from a cytoband annotation track an 'annotation' column name, to list 'annotation' elements overlapping each .self element - fuzziness : single integer value, to be added on each side of .self elements when computing overlaps. - maxElements : single integer value, when more overlaps are found, lists are replaced by counts. Can be NA to disable this behavior. - location : character vector, the 'chrom' / 'start' / 'end' .self columns to use for annotation. - precision : single integer value from 1 to 4, amount of digits to consider in banding (type='cytoband'). - quiet : single logical value, wether to throw progression messages or not.
The following methods are inherited (from the corresponding class):
  • callParams ()
  • callSuper ()
  • check ()
  • chromosomes ()
  • copy ()
  • defaultParams ()
  • draw ()
  • export ()
  • field ()
  • fix.param ()
  • getChromEnd ()
  • getClass ()
  • getName ()
  • getParam ()
  • getRefClass ()
  • import ()
  • initFields ()
  • initialize ()
  • setName ()
  • setParam ()
  • show ()
  • slice ()
  • trace ()
  • untrace ()
  • usingMethods ()

See Also

, , , cghRA.array