Identification of Cancer Dysfunctional Subpathway with Omics Data

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Documentation for package ‘ICDS’ version 0.1.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

ICDS-package	Identification of Cancer Dysfunctional Subpathway by integrating DNA methylation, copy number variation, and gene expression data
amp_gene	The variables in the environment include an example expression profile,an methylation profile,an copy number variation data,amplified genes,deleted genes,A numeric vector of z_scores,p-values,A vector of 0/1s, indicating the class of samples,interested subpathways,Optimized subpathway,and the statistical significance p value and FDR for these optimal subpathways
cnv.p	The variables in the environment include an example expression profile,an methylation profile,an copy number variation data,amplified genes,deleted genes,A numeric vector of z_scores,p-values,A vector of 0/1s, indicating the class of samples,interested subpathways,Optimized subpathway,and the statistical significance p value and FDR for these optimal subpathways
cnv_data	The variables in the environment include an example expression profile,an methylation profile,an copy number variation data,amplified genes,deleted genes,A numeric vector of z_scores,p-values,A vector of 0/1s, indicating the class of samples,interested subpathways,Optimized subpathway,and the statistical significance p value and FDR for these optimal subpathways
combinep_three	combinep_three
combinep_two	combinep_two
coverp2zscore	coverp2zscore
del_gene	The variables in the environment include an example expression profile,an methylation profile,an copy number variation data,amplified genes,deleted genes,A numeric vector of z_scores,p-values,A vector of 0/1s, indicating the class of samples,interested subpathways,Optimized subpathway,and the statistical significance p value and FDR for these optimal subpathways
envData	The variables in the environment include an example expression profile,an methylation profile,an copy number variation data,amplified genes,deleted genes,A numeric vector of z_scores,p-values,A vector of 0/1s, indicating the class of samples,interested subpathways,Optimized subpathway,and the statistical significance p value and FDR for these optimal subpathways
exp.p	The variables in the environment include an example expression profile,an methylation profile,an copy number variation data,amplified genes,deleted genes,A numeric vector of z_scores,p-values,A vector of 0/1s, indicating the class of samples,interested subpathways,Optimized subpathway,and the statistical significance p value and FDR for these optimal subpathways
exp_data	The variables in the environment include an example expression profile,an methylation profile,an copy number variation data,amplified genes,deleted genes,A numeric vector of z_scores,p-values,A vector of 0/1s, indicating the class of samples,interested subpathways,Optimized subpathway,and the statistical significance p value and FDR for these optimal subpathways
FindSubPath	FindSubPath
getCnvp	getCnvp
GetExampleData	Get the example data
getExpp	getExpp
getMethp	getMethp
ICDS	Identification of Cancer Dysfunctional Subpathway by integrating DNA methylation, copy number variation, and gene expression data
label1	The variables in the environment include an example expression profile,an methylation profile,an copy number variation data,amplified genes,deleted genes,A numeric vector of z_scores,p-values,A vector of 0/1s, indicating the class of samples,interested subpathways,Optimized subpathway,and the statistical significance p value and FDR for these optimal subpathways
label2	The variables in the environment include an example expression profile,an methylation profile,an copy number variation data,amplified genes,deleted genes,A numeric vector of z_scores,p-values,A vector of 0/1s, indicating the class of samples,interested subpathways,Optimized subpathway,and the statistical significance p value and FDR for these optimal subpathways
meth.p	The variables in the environment include an example expression profile,an methylation profile,an copy number variation data,amplified genes,deleted genes,A numeric vector of z_scores,p-values,A vector of 0/1s, indicating the class of samples,interested subpathways,Optimized subpathway,and the statistical significance p value and FDR for these optimal subpathways
meth_data	The variables in the environment include an example expression profile,an methylation profile,an copy number variation data,amplified genes,deleted genes,A numeric vector of z_scores,p-values,A vector of 0/1s, indicating the class of samples,interested subpathways,Optimized subpathway,and the statistical significance p value and FDR for these optimal subpathways
opt_subpath	opt_subpath
opt_subpathways	The variables in the environment include an example expression profile,an methylation profile,an copy number variation data,amplified genes,deleted genes,A numeric vector of z_scores,p-values,A vector of 0/1s, indicating the class of samples,interested subpathways,Optimized subpathway,and the statistical significance p value and FDR for these optimal subpathways
Permutation	Permutation
PlotSubpathway	PlotSubpathway
subpathdata	The variables in the environment include an example expression profile,an methylation profile,an copy number variation data,amplified genes,deleted genes,A numeric vector of z_scores,p-values,A vector of 0/1s, indicating the class of samples,interested subpathways,Optimized subpathway,and the statistical significance p value and FDR for these optimal subpathways
zzz	The variables in the environment include an example expression profile,an methylation profile,an copy number variation data,amplified genes,deleted genes,A numeric vector of z_scores,p-values,A vector of 0/1s, indicating the class of samples,interested subpathways,Optimized subpathway,and the statistical significance p value and FDR for these optimal subpathways