opt_subpath

`opt_subpath` Optimize interested subpathways.If the number of genes shared by the two pathways accounted for more than the Overlap ratio of each pathway genes,then combine two pathways.

Identify Cancer Dysfunctional Sub-pathway by integrating gene expression, DNA methylation and copy number variation, and pathway topological information. 1)We firstly calculate the gene risk scores by integrating three kinds of data: DNA methylation, copy number variation, and gene expression.  2)Secondly, we perform a greedy search algorithm to identify the key dysfunctional sub-pathways within the pathways for which the discriminative scores were locally maximal. 3)Finally, the permutation test was used to calculate statistical significance level for these key dysfunctional sub-pathways.

Junwei Han

ICDS

Identification of Cancer Dysfunctional Subpathway with Omics
Data

Baotong Zheng

Siyao Liu

opt_subpath function

<dl><dt>subpathdata</dt>
<dd>interested subpathways</dd>
<dt>zz</dt>
<dd>a vector of z-scores</dd>
<dt>overlap</dt>
<dd>Overlap ratio of each two pathway genes</dd></dl>

Arguments

opt_subpath — opt_subpath

<dl>

<dt>subpathdata</dt>
<dd>interested subpathways</dd>


<dt>zz</dt>
<dd>a vector of z-scores</dd>


<dt>overlap</dt>
<dd>Overlap ratio of each two pathway genes</dd>

</dl>

opt_subpath: opt_subpath

Description

Usage

Value

Arguments

Examples