Chain-class {rtracklayer} | R Documentation

## 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 `IntegerRanges` 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 `ChainBlock`s. Alignments for chromosomes matching the `exclude` pattern are not imported.

### Note

A chain file essentially details many local alignments, so it is possible for the "from" ranges to map to overlapping regions in the other sequence. The "from" ranges are guaranteed to be disjoint (but do not necessarily cover the entire "from" sequence).

### Author(s)

Michael Lawrence

### See Also

`liftOver` for performing lift overs using a chain alignment

[Package rtracklayer version 1.52.1 Index]