Package: ICDS
Type: Package
Title: Identification of Cancer Dysfunctional Subpathway with Omics
        Data
Version: 0.1.3
Authors@R: c(
    person("Junwei", "Han", email = "hanjunwei1981@163.com", role = "cre"),
    person("Baotong", "Zheng", email = "btzheng1116@163.com", role = "aut"),
    person("Siyao", "Liu", email = "liusiyao29@163.com", role = "ctb"))
Maintainer: Junwei Han <hanjunwei1981@163.com>
Description: 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.
Depends: R (>= 4.3.0)
biocViews:
Imports: igraph, graphite, metap, methods, org.Hs.eg.db
Suggests: knitr, rmarkdown
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2024-08-01 06:56:52 UTC; btzheng
Author: Junwei Han [cre],
  Baotong Zheng [aut],
  Siyao Liu [ctb]
Repository: CRAN
Date/Publication: 2024-08-01 09:40:02 UTC
Built: R 4.5.2; ; 2025-11-08 04:23:12 UTC; windows
