Identification of Cancer Dysfunctional Subpathway by Integrating DNA Methylation, Copy Number Variation, and Gene Expression Data

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.


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0.1.1 by Junwei Han, 2 years ago

Browse source code at

Authors: Junwei Han , Baotong Zheng , Siyao Liu

Documentation:   PDF Manual  

GPL (>= 2) license

Imports igraph, graphite, metap, methods,

Suggests knitr, rmarkdown, prettydoc

See at CRAN