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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.
| Version: | 0.1.3 |
| Depends: | R (≥ 4.3.0) |
| Imports: | igraph, graphite, metap, methods, org.Hs.eg.db |
| Suggests: | knitr, rmarkdown |
| Published: | 2024-08-01 |
| DOI: | 10.32614/CRAN.package.ICDS |
| Author: | Junwei Han [cre], Baotong Zheng [aut], Siyao Liu [ctb] |
| Maintainer: | Junwei Han <hanjunwei1981 at 163.com> |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| NeedsCompilation: | no |
| Citation: | ICDS citation info |
| Materials: | README |
| In views: | Omics |
| CRAN checks: | ICDS results |
| Reference manual: | ICDS.pdf |
| Vignettes: |
ICDS User Guide (source, R code) |
| Package source: | ICDS_0.1.3.tar.gz |
| Windows binaries: | r-devel: ICDS_0.1.3.zip, r-release: ICDS_0.1.3.zip, r-oldrel: ICDS_0.1.3.zip |
| macOS binaries: | r-release (arm64): ICDS_0.1.3.tgz, r-oldrel (arm64): ICDS_0.1.3.tgz, r-release (x86_64): ICDS_0.1.3.tgz, r-oldrel (x86_64): ICDS_0.1.3.tgz |
| Old sources: | ICDS archive |
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