findNull

In tumor tissue, underlying genomic instability can lead to DNA copy number alterations,
e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the
genome, whereas recurrent alterations are observed in the same genomic region across multiple
independent samples, perhaps because they provide a selective growth advantage. Here we use
cyclic shift permutations to identify recurrent copy number alterations in a single cohort or
recurrent copy number differences in two cohorts based on a common set of genomic markers.
Additional functionality is provided to perform downstream analyses, including the creation of
summary files and graphics. DiNAMIC.Duo builds upon the original DiNAMIC package of Walter et al.
(2011) <doi:10.1093/bioinformatics/btq717> and leverages the theory developed in Walter et al.
(2015) <doi:10.1093/biomet/asv046>. An article describing DiNAMIC.Duo by Walter et al. (2022)
can be found at <doi: 10.1093/bioinformatics/btac542>.

Vonn Walter

DiNAMIC.Duo

Finding Recurrent DNA Copy Number Alterations and Differences

Hyo Young Choi

Xiaobei Zhao

Yan Gao

David Neil Hayes

findNull function

<dl><dt>x</dt>
<dd>An n by m numeric matrix containing DNA copy number data from n subjects at m markers.</dd>
<dt>num.perms</dt>
<dd>A positive integer that represents the number of cyclic shifts used to create
the empirical distribution.</dd>
<dt>random.seed</dt>
<dd>An optional random seed (default = NULL).</dd></dl>

Arguments

Find DiNAMIC's null distribution — findNull

<dl>

<dt>x</dt>
<dd>An n by m numeric matrix containing DNA copy number data from n subjects at m markers.</dd>


<dt>num.perms</dt>
<dd>A positive integer that represents the number of cyclic shifts used to create
the empirical distribution.</dd>


<dt>random.seed</dt>
<dd>An optional random seed (default = NULL).</dd>

</dl>

Find DiNAMIC's null distribution

findNull: Find DiNAMIC's null distribution

Description

Usage

Value

Arguments

Details

Examples