testROH.numeric

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

Frank E Harrell Jr

testROH.numeric function

<dl> <dt>muN</dt>
<dd>An <code><a href="/link/numeric?package=PSCBS&version=0.68.0" data-mini-rdoc="PSCBS::numeric">numeric</a></code> <code><a href="/link/vector?package=PSCBS&version=0.68.0" data-mini-rdoc="PSCBS::vector">vector</a></code> of J genotype calls in
 {0,1/2,1} for AA, AB, and BB, respectively,
 and <code><a href="/link/NA?package=PSCBS&version=0.68.0" data-mini-rdoc="PSCBS::NA">NA</a></code> for non-polymorphic loci.</dd> <dt>csN</dt>
<dd>(optional) A <code><a href="/link/numeric?package=PSCBS&version=0.68.0" data-mini-rdoc="PSCBS::numeric">numeric</a></code> <code><a href="/link/vector?package=PSCBS&version=0.68.0" data-mini-rdoc="PSCBS::vector">vector</a></code> of J genotype confidence scores.
 If <code><a href="/link/NULL?package=PSCBS&version=0.68.0" data-mini-rdoc="PSCBS::NULL">NULL</a></code>, ad hoc scores calculated from <code>betaN</code> are used.</dd> <dt>betaN</dt>
<dd>(optional) A <code><a href="/link/numeric?package=PSCBS&version=0.68.0" data-mini-rdoc="PSCBS::numeric">numeric</a></code> <code><a href="/link/vector?package=PSCBS&version=0.68.0" data-mini-rdoc="PSCBS::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 href="/link/NA?package=PSCBS&version=0.68.0" data-mini-rdoc="PSCBS::NA">NA</a></code> for non-polymorphic loci.</dd> <dt>minNbrOfSnps</dt>
<dd>Minimum number of SNPs required to test segment.
 If not tested, <code><a href="/link/NA?package=PSCBS&version=0.68.0" data-mini-rdoc="PSCBS::NA">NA</a></code> is returned.</dd> <dt>delta</dt>
<dd>A <code><a href="/link/double?package=PSCBS&version=0.68.0" data-mini-rdoc="PSCBS::double">double</a></code> scalar specifying the maximum (weighted)
 proportion of heterozygous SNPs allowed in an ROH region.</dd> <dt>...</dt>
<dd>Not used.</dd> <dt>verbose</dt>
<dd>See <code>Verbose</code>.</dd></dl>

Arguments

Author

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

<dl>

 <dt>muN</dt>
<dd>An <code><a href='https://rdrr.io/r/base/numeric.html'>numeric</a></code> <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> of J genotype calls in
 {0,1/2,1} for AA, AB, and BB, respectively,
 and <code><a href='https://rdrr.io/r/base/NA.html'>NA</a></code> for non-polymorphic loci.</dd>

 <dt>csN</dt>
<dd>(optional) A <code><a href='https://rdrr.io/r/base/numeric.html'>numeric</a></code> <code><a href='https://rdrr.io/r/base/vector.html'>vector</a></code> of J genotype confidence scores.
 If <code><a href='https://rdrr.io/r/base/NULL.html'>NULL</a></code>, ad hoc scores calculated from <code>betaN</code> are used.</dd>

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

 <dt>minNbrOfSnps</dt>
<dd>Minimum number of SNPs required to test segment.
 If not tested, <code><a href='https://rdrr.io/r/base/NA.html'>NA</a></code> is returned.</dd>

 <dt>delta</dt>
<dd>A <code><a href='https://rdrr.io/r/base/double.html'>double</a></code> scalar specifying the maximum (weighted)
 proportion of heterozygous SNPs allowed in an ROH region.</dd>

 <dt>...</dt>
<dd>Not used.</dd>

 <dt>verbose</dt>
<dd>See <code>Verbose</code>.</dd>

</dl>

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

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

Description

Usage

Value

Arguments

Author