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PSCBS (version 0.45.1)

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

Description

Identifies gaps of a genome where there exist no observations.

Usage

## S3 method for class 'default':
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.

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.