testROH.numeric

An <code><a rd-options="base" href="/link/numeric?package=PSCBS&version=0.63.0&to=base" data-mini-rdoc="base::numeric">numeric</a></code> <code><a rd-options="base" href="/link/vector?package=PSCBS&version=0.63.0&to=base" data-mini-rdoc="base::vector">vector</a></code> of J genotype calls in
 {0,1/2,1} for AA, AB, and BB, respectively,
 and <code><a rd-options="base" href="/link/NA?package=PSCBS&version=0.63.0&to=base" data-mini-rdoc="base::NA">NA</a></code> for non-polymorphic loci.

(optional) A <code><a rd-options="base" href="/link/numeric?package=PSCBS&version=0.63.0&to=base" data-mini-rdoc="base::numeric">numeric</a></code> <code><a rd-options="base" href="/link/vector?package=PSCBS&version=0.63.0&to=base" data-mini-rdoc="base::vector">vector</a></code> of J genotype confidence scores.
 If <code><a rd-options="base" href="/link/NULL?package=PSCBS&version=0.63.0&to=base" data-mini-rdoc="base::NULL">NULL</a></code>, ad hoc scores calculated from <code>betaN</code> are used.

(optional) A <code><a rd-options="base" href="/link/numeric?package=PSCBS&version=0.63.0&to=base" data-mini-rdoc="base::numeric">numeric</a></code> <code><a rd-options="base" href="/link/vector?package=PSCBS&version=0.63.0&to=base" data-mini-rdoc="base::vector">vector</a></code> of J matched normal BAFs
 in [0,1] (due to noise, values may be slightly outside as well)
 or <code><a rd-options="base" href="/link/NA?package=PSCBS&version=0.63.0&to=base" data-mini-rdoc="base::NA">NA</a></code> for non-polymorphic loci.

betaN

Minimum number of SNPs required to test segment.
 If not tested, <code><a rd-options="base" href="/link/NA?package=PSCBS&version=0.63.0&to=base" data-mini-rdoc="base::NA">NA</a></code> is returned.

minNbrOfSnps

A <code><a rd-options="base" href="/link/double?package=PSCBS&version=0.63.0&to=base" data-mini-rdoc="base::double">double</a></code> scalar specifying the maximum (weighted)
 proportion of heterozygous SNPs allowed in an ROH region.

delta

See <code><a rd-options="R.utils" href="/link/Verbose?package=PSCBS&version=0.63.0&to=R.utils" data-mini-rdoc="R.utils::Verbose">Verbose</a></code>.

verbose

Tests if a segment is in Run-of-Homozygosity (ROH).

methods

internal

Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome.  Both tumor-normal paired and tumor-only analyses are supported.

Henrik Bengtsson

PSCBS

Analysis of Parent-Specific DNA Copy Numbers

Pierre Neuvial

Venkatraman E. Seshan

Adam B. Olshen

Paul T. Spellman

Richard A. Olshen

testROH.numeric function

An <code><a rd-options='base' href='numeric'>numeric</a></code> <code><a rd-options='base' href='vector'>vector</a></code> of J genotype calls in
 {0,1/2,1} for AA, AB, and BB, respectively,
 and <code><a rd-options='base' href='NA'>NA</a></code> for non-polymorphic loci.

(optional) A <code><a rd-options='base' href='numeric'>numeric</a></code> <code><a rd-options='base' href='vector'>vector</a></code> of J genotype confidence scores.
 If <code><a rd-options='base' href='NULL'>NULL</a></code>, ad hoc scores calculated from <code>betaN</code> are used.

(optional) A <code><a rd-options='base' href='numeric'>numeric</a></code> <code><a rd-options='base' href='vector'>vector</a></code> of J matched normal BAFs
 in [0,1] (due to noise, values may be slightly outside as well)
 or <code><a rd-options='base' href='NA'>NA</a></code> for non-polymorphic loci.

Minimum number of SNPs required to test segment.
 If not tested, <code><a rd-options='base' href='NA'>NA</a></code> is returned.

A <code><a rd-options='base' href='double'>double</a></code> scalar specifying the maximum (weighted)
 proportion of heterozygous SNPs allowed in an ROH region.

See <code><a rd-options='R.utils' href='Verbose'>Verbose</a></code>.

testROH.numeric: Tests if a segment is in Run-of-Homozygosity (ROH)

Description

Usage

Arguments

Value