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SmCCNet (version 2.0.3)

Sparse Multiple Canonical Correlation Network Analysis Tool

Description

A canonical correlation based framework (SmCCNet) designed for the construction of phenotype-specific multi-omics networks. This framework adeptly integrates single or multiple omics data types along with a quantitative or binary phenotype of interest. It offers a streamlined setup process that can be tailored manually or configured automatically, ensuring a flexible and user-friendly experience.

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Version

Install

install.packages('SmCCNet')

Monthly Downloads

25

Version

2.0.3

License

GPL-3

Issues

1

Pull Requests

0

Stars

32

Forks

5

Maintainer

Weixuan Liu

Last Published

April 16th, 2024

Functions in SmCCNet (2.0.3)

getRobustWeightsMultiBinary

Run Sparse multiple Canonical Correlation Analysis and Obtain Canonical Weights (with Subsampling)
Y

A synthetic phenotype dataset.
fastAutoSmCCNet

Automated SmCCNet to Streamline the SmCCNet Pipeline
aggregateCVSingle

Aggregate and Save Cross-validation Result for Single-omics Analysis
dataPreprocess

preprocess a omics dataset before running omics SmCCNet
classifierEval

Evaluation of Binary Classifier with Different Evaluation Metrics
getAbar

Calculate similarity matrix based on canonical weights.
getCanCorMulti

Canonical Correlation Value for SmCCA
getRobustWeightsMulti

Run Sparse multiple Canonical Correlation Analysis and Obtain Canonical Weights (with Subsampling)
getCanWeightsMulti

Get Canonical Weight SmCCA Algorithm (No Subsampling)
scalingFactorInput

Scaling Factor Input Prompt
getOmicsModules

Extract Omics Modules based on Similarity Matrix.
getRobustWeightsSingle

Single-omics SmCCA with Quantitative Phenotype
getRobustWeightsSingleBinary

Single-omics SmCCA with Binary Phenotype
summarizeNetSHy

NetSHy Summarization Score
networkPruning

Prunes Subnetwork and Return Final Pruned Subnetwork Module
%>%

Pipe operator
X1

A synthetic mRNA expression dataset.
getCCAout_single

Internal functions called by getRobustPseudoWeights_single.
X2

A synthetic miRNA expression dataset.