callSegmentationOutliers.default

callSegmentationOutliers

A <code><a href="/link/numeric?package=PSCBS&version=0.12.2&to=base" rd-options="base" data-mini-rdoc="base::numeric">numeric</a></code> <code><a href="/link/vector?package=PSCBS&version=0.12.2&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> of J genomic signals to be segmented.

(Optional) An <code><a href="/link/integer?package=PSCBS&version=0.12.2&to=base" rd-options="base" data-mini-rdoc="base::integer">integer</a></code> scalar
       (or a <code><a href="/link/vector?package=PSCBS&version=0.12.2&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> of length J contain a unique value).
       Only used for annotation purposes.

chromosome

Optional <code><a href="/link/numeric?package=PSCBS&version=0.12.2&to=base" rd-options="base" data-mini-rdoc="base::numeric">numeric</a></code> <code><a href="/link/vector?package=PSCBS&version=0.12.2&to=base" rd-options="base" data-mini-rdoc="base::vector">vector</a></code> of J genomic locations.
            If <code><a href="/link/NULL?package=PSCBS&version=0.12.2&to=base" rd-options="base" data-mini-rdoc="base::NULL">NULL</a></code>, index locations <code>1:J</code>

A <code><a href="/link/character?package=PSCBS&version=0.12.2&to=base" rd-options="base" data-mini-rdoc="base::character">character</a></code> string specifying the Method
        used for calling outliers.

method

Additional arguments passed to internal outlier
        detection method.

See <code><a href="/link/Verbose?package=PSCBS&version=0.12.2&to=R.utils" rd-options="R.utils" data-mini-rdoc="R.utils::Verbose">Verbose</a></code>.

verbose

Calls single-locus outliers along the genome that have a signal that differ significantly from the
  neighboring loci.

Segments allele-specific DNA copy number data to detect
        regions with abnormal copy number within each parental
        chromosome

Henrik Bengtsson

PSCBS

Analysis of Parent-Specific DNA Copy Numbers

callSegmentationOutliers function

Signals as well as genomic positions may contain missing
   values, i.e. <code><a href="/link/NA?package=PSCBS&version=0.12.2&to=base" rd-options="base" data-mini-rdoc="base::NA">NA</a></code>s or <code><a href="/link/NaN?package=PSCBS&version=0.12.2&to=base%3Ais.finite" rd-options="base:is.finite" data-mini-rdoc="base:is.finite::NaN">NaN</a></code>s.  By definition, these cannot
   be outliers.

callSegmentationOutliers: Calls single-locus outliers along the genome

Description

Usage

Arguments

Value

Missing and non-finite values

See Also