crossable-class: Class '"crossable"'

In Rgb: The R Genome Browser

Class "crossable"

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 "track.table", as "sliceable" does not guarantee that slice returns a data.frame as crossable needs one.

Extends

Class sliceable, directly.
Class drawable, by class sliceable, distance 2.

All reference classes extend and inherit methods from envRefClass.

Fields

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

• name (drawable)

• parameters (drawable)

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 (drawable)

• callSuper (envRefClass)

• check (drawable)

• chromosomes (drawable)

• copy (envRefClass)

• defaultParams (sliceable)

• draw (sliceable)

• export (envRefClass)

• field (envRefClass)

• fix.param (drawable)

• getChromEnd (sliceable)

• getClass (envRefClass)

• getName (drawable)

• getParam (drawable)

• getRefClass (envRefClass)

• import (envRefClass)

• initFields (envRefClass)

• initialize (drawable)

• setName (drawable)

• setParam (drawable)

• show (sliceable)

• slice (sliceable)

• trace (envRefClass)

• untrace (envRefClass)

• usingMethods (envRefClass)

Author(s)

Sylvain Mareschal

See Also

drawable, sliceable, track.table, cghRA.array

Rgb documentation built on Aug. 18, 2023, 5:05 p.m.