GenomicVariation-class

GenomicVariation

S4 class for storing summarized genomic variation profile.

Contains functions for identification of
copy number signatures (Geoffrey et al. (2018) <doi:10.1038/s41588-018-0179-8>) and
mutation signatures (Alexandrov et al. (2013) <doi:10.1038/nature12477>)
by non-negative matrix factorization, signature analysis and visualization.
It can be used to capture signatures of genomic variation, compare genotype or
phenotype features of different signatures and thus uncover the relationship
between the mechanism of genomic variation and phenotypes in cancer.

Shixiang Wang

sigminer

Capture Genomic Variation Signatures using Non-Negative Matrix
Factorization

Geoffrey Macintyre

Xue-Song Liu

GenomicVariation-class function

<dl class="dl-horizontal">
<dt><code>CopyNumber</code></dt><dd>a <code>CopyNumber</code> object.</dd></dl><dt><code>MAF</code></dt><dd>a <code>MAF</code> object.</dd><dt><code>clinical.data</code></dt><dd>data associated with each sample in copy number profile
and MAF. This slot is intersection of <code>clinical.data</code> slot in both <code>CopyNumber</code>
object and <code>MAF</code> object.</dd>

GenomicVariation-class: Class GenomicVariation

Description

Arguments

Slots