Differential Network Analysis using Gene Pathways
Combine two 'dnapath_list' objects.
Combine two 'dnapath' objects.
Modify a pathway list to combine overlapping pathways.
C++ implementation of d_edges
C++ implementation of d_genes
C++ implementation of d_pathway
Differential network analysis on a single pathway
Differential Network Analysis Using Gene Pathways
Obtain gene symbols for entrezgene IDs
Remove pathways with non-significant DC scores.
Format sepcies name input.
Internal function for obtaining biomaRt mapping
Get the gene names from a differential network analysis
Get mean expression of pathway genes in both groups
Get the minimum alpha level for the permutation test
Get the two association networks
Obtain Reactome pathways
Return the first part of the dnapath results.
Initialize biomaRt for a given species
The number of pathways in a 'dnapath_list' object.
The pathway names in a 'dnapath_list' object.
The pathway names in a 'dnapath' object.
Plot the expression values of two genes
Plot function for 'dnapath' object.
Print function for 'dnapath_list' object.
Print function for 'dnapath' object.
Rename genes in the differential network analysis
Reverse the order of pathways in a 'dnapath_list' object.
Wrapper for ARACNE method
Wrapper for BC3Net method
Wrapper for C3Net method
Wrapper for CLR method
Wrapper for correlation co-expression
Wrapper for GENIE3 method
Wrapper for glasso method
Wrapper for MRNET method
Wrapper for partial correlations with Empirical Bayes FDR correction
Wrapper for partial correlations from corpcor
Wrapper for silencer method
Sort function for 'dnapath_list' object.
Extract parts of a 'dnapath_list' object.
Extract results of a single pathway from a 'dnapath' object.
Extract results of a single pathway from a 'dnapath_list' object.
Extract results of a single pathway from a 'dnapath' object.
Replace parts of a 'dnapath_list' object.
Replace parts of a 'dnapath' object.
Subset function for 'dnapath_list' object.
Summarize differential connections for a pathway
Summarize differential connectivity of genes in a pathway
Summarize the differential connectivity of genes over all pathways.
Summarize the differential connectivity of pathways.
Summary function for 'dnapath_list' object.
Summary function for 'dnapath' object.
Obtain entrezgene IDs for gene symbols
Return the last part of the dnapath results.
Integrates pathway information into the differential network analysis of two gene expression datasets as described in Grimes, Potter, and Datta (2019) <doi:10.1038/s41598-019-41918-3>. Provides summary functions to break down the results at the pathway, gene, or individual connection level. The differential networks for each pathway of interest can be plotted, and the visualization will highlight any differentially expressed genes and all of the gene-gene associations that are significantly differentially connected.