cyclicShiftColR

Perform the cyclic shift procedure on the columns of a matrix

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

cyclicShiftColR function

<dl><dt>X</dt>
<dd>a matrix or a data frame of copy number data. The rows and columns
of X correspond to genes and subjects, respectively.</dd>
<dt>randomSeed</dt>
<dd>a random seed. Default = NULL.</dd></dl>

Arguments

Perform the cyclic shift procedure on the columns of a matrix — cyclicShiftColR

<dl>

<dt>X</dt>
<dd>a matrix or a data frame of copy number data. The rows and columns
of X correspond to genes and subjects, respectively.</dd>


<dt>randomSeed</dt>
<dd>a random seed. Default = NULL.</dd>

</dl>

cyclicShiftColR: Perform the cyclic shift procedure on the columns of a matrix

Description

Usage

Value

Arguments

Details

Examples