genomeSegment-class {rtracklayer}R Documentation

Class "genomeSegment"

Description

An object representing a segment of a genome.

Objects from the Class

Objects are normally created by a call of the following form: genomeSegment(genome, chrom, start, end, segment). All parameters are optional and correspond to slots of the new genomeSegment instance, except for the segment parameter, which serves as the base for the new instance. The slots of the new segment match those of segment, unless the call specifies other parameters, which override the corresponding slots in segment.

Slots

genome:
Object of class "character" giving the name of the genome (e.g. "hg18").
chrom:
Object of class "character" giving the chromosome name (e.g. "chr22").
start:
Object of class "numeric" indicating the start position of the segment on the chromosome.
end:
Object of class "numeric" indicating the stop position of the segment on the chromosome.

Methods

merge(x, y)
Merges two instances. The result has the same slot values as x, except the non-empty slots in y override those from x.
genome(object)
Gets the genome identifier.
genome(object) <- value
Sets the genome identifier.
chrom(object)
Gets the chromosome identifier.
chrom(object) <- value
Sets the chromosome identifier.
start(object)
Gets the start position.
start(object) <- value
Sets the start position.
end(object)
Gets the end position.
end(object) <- value
Sets the end position.
object / x
Zoom out x times (expand segment by x/2 on each side).
object * x
Zoom in x times (contract segment by x/2 on each side).

Author(s)

Michael Lawrence

See Also

genomeSegment for obtaining instances of this class.


[Package rtracklayer version 1.2.2 Index]