class:Chain

Chain-class

ChainBlock-class

class:ChainBlock

class:ChainFile

ChainFile-class

import.chain

import.chain,ANY-method

import,ChainFile,ANY,ANY-method

ChainFile

ranges,ChainBlock-method

offset,ChainBlock-method

score,ChainBlock-method

space,ChainBlock-method

reversed

reversed,ChainBlock-method

A <code>Chain</code> object represents a UCSC chain alignment, typically
  imported from a <code>chain</code> file, and is essentially a list of
  <code>ChainBlock</code> objects. Each <code>ChainBlock</code> has a corresponding
  chromosome (its name in the list) and is a run-length
  encoded alignment, mapping a set of intervals on that chromosome to
  intervals on the same or other chromosomes.

classes

methods

Extensible framework for interacting with multiple genome 
  browsers (currently UCSC built-in) and manipulating 
  annotation tracks in various formats (currently GFF, BED, bedGraph, BED15,
  WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the
  supported browsers, as well as query and modify the browser state, such as the
  current viewport.

Chain-class: Chain objects

Description

Arguments

See Also