findLargeGaps: Identifies gaps of a genome where there exist no observations

In HenrikBengtsson/PSCBS: Analysis of Parent-Specific DNA Copy Numbers

Identifies gaps of a genome where there exist no observations

Description

Identifies gaps of a genome where there exist no observations.

Usage

## Default S3 method:
findLargeGaps(chromosome=NULL, x, minLength, resolution=1L, ...)

Arguments

chromosome	(Optional) An integer vector of length J of chromosome indices.
x	A numeric vector of J of genomic locations.
minLength	A positive numeric scalar specifying the minimum length of a gap.
resolution	A non-negative numeric specifying the minimum length unit, which by default equals one nucleotide/base pair.
...	Not used.

Value

Returns data.frame zero or more rows and with columns chromosome (if given), start, stop, and length.

Author(s)

Henrik Bengtsson

See Also

Use gapsToSegments() to turn the set of identified gaps into the complementary set of segments such that they can be passed to segmentByCBS(), segmentByPairedPSCBS() and segmentByNonPairedPSCBS() via argument knownSegments.

HenrikBengtsson/PSCBS documentation built on Feb. 20, 2024, 9:01 p.m.