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ICDS  

Identification of Cancer Dysfunctional Subpathway with Omics Data
View on CRAN: Click here


Download and install ICDS package within the R console
Install from CRAN:
install.packages("ICDS")

Install from Github:
library("remotes")
install_github("cran/ICDS")

Install by package version:
library("remotes")
install_version("ICDS", "0.1.3")



Attach the package and use:
library("ICDS")
Maintained by
Junwei Han
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-01-25
Latest Update: 2021-07-15
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.
How to cite:
Junwei Han (2019). ICDS: Identification of Cancer Dysfunctional Subpathway with Omics Data. R package version 0.1.3, https://cran.r-project.org/web/packages/ICDS. Accessed 21 Nov. 2024.
Previous versions and publish date:
0.1.1 (2019-01-25 18:00), 0.1.2 (2021-07-15 13:30)
Other packages that cited ICDS R package
View ICDS citation profile
Other R packages that ICDS depends, imports, suggests or enhances
Complete documentation for ICDS
Functions, R codes and Examples using the ICDS R package
Some associated functions: FindSubPath . GetExampleData . ICDS-package . Permutation . PlotSubpathway . combinep_three . combinep_two . coverp2zscore . envData . getCnvp . getExpp . getMethp . opt_subpath . 
Some associated R codes: GetExampleData.R . ICDS-package.R . OptimalSubpath.R . getEnvironmentData.R . getp.R .  Full ICDS package functions and examples
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