Chain-class: Chain objects
Description
A Chain object represents a UCSC chain alignment, typically
imported from a chain file, and is essentially a list of
ChainBlock objects. Each ChainBlock 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.
Accessor Methods
In the code snippets below, x and object are
ChainBlock objects.
-
ranges(x):
Get the Ranges object holding
the starts and ends of the "from" ranges. Each range is a
contiguous block of positions aligned without gaps to the other
sequence.
-
offset(x): Integer offset from the "from" start to the
"end" start (which could be in another chromosome).
-
score(x): The score for each mapping.
-
space(x): The space (chromosome) of the "to" range.
-
reversed(x): Whether the mapping inverts the region, i.e.,
the alignment is between different strands.
Import
A Chain object can be loaded from a UCSC chain format file
simply by passing the path import function. If the file
extension is not “chain”, then either pass “chain” to
the format argument, or cast the path to a ChainFile
object. The import.chain function is provided as a (slight)
convenience. It is documented below, along with the extra
exclude argument to the import method.
-
import.chain(con, exclude = "_", ...):
Imports a chain file named con as a Chain object, a
list of ChainBlocks. Alignments for chromosomes matching the
exclude pattern are not imported.
See Also
liftOver for performing lift overs using a chain alignment