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.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):
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