segmentMap-class: Class '"segmentMap"'

In cghRA: Array CGH Data Analysis and Visualization

Description

Efficient storage of a large collection of genomic intervals, located using probe IDs from a specific array design rather than genomic coordinates. Objects of this class are essentially intended to be produced by the map2design function, and used by the cnvScore function.

Extends

All reference classes extend and inherit methods from envRefClass.

Fields

designName:

Single character value, the content of the name field of the cghRA.design object used to produce the object.

designSize:

Single integer value, the row count in the cghRA.design object used to produce the object.

map:

Integer matrix with one row for each distinct genomic interval in the mapped track.table object. The columns are start and end, the indexes of the first and last design elements in the interval and count, the amount of such intervals in the mapped object. Row names of this matrix list the indexes of the corresponding mapped object intervals.

trackName:

Single character value, the content of the name field of the mapped track.table object.

trackSize:

Single integer value, the row count in the mapped track.table object.

Methods

check(warn = ):

Raises an error if the object is not valid, else returns TRUE

initialize(map = , trackName = , trackSize = , designName = , designSize = , ...):

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

• callSuper (envRefClass)

• copy (envRefClass)

• export (envRefClass)

• field (envRefClass)

• getClass (envRefClass)

• getRefClass (envRefClass)

• import (envRefClass)

• initFields (envRefClass)

• show (envRefClass, overloaded)

• trace (envRefClass)

• untrace (envRefClass)

• usingMethods (envRefClass)

Author(s)

Sylvain Mareschal

See Also

map2design, cnvScore

cghRA documentation built on May 2, 2019, 3:34 a.m.