[.dnapath               Extract results of a single pathway from a
                        'dnapath' object.
[.dnapath_list          Extract parts of a 'dnapath_list' object.
[<-.dnapath             Replace parts of a 'dnapath' object.
[<-.dnapath_list        Replace parts of a 'dnapath_list' object.
[[.dnapath              Extract results of a single pathway from a
                        'dnapath' object.
[[.dnapath_list         Extract results of a single pathway from a
                        'dnapath_list' object.
biomart_hsapiens        Default mapping for entrezgene IDs and HGNC
                        gene symbols
c.dnapath               Combine two 'dnapath' objects.
c.dnapath_list          Combine two 'dnapath_list' objects.
d_edgesC                C++ implementation of d_edges
d_genesC                C++ implementation of d_genes
d_pathwayC              C++ implementation of d_pathway
dnapath                 Differential Network Analysis Using Gene
                        Pathways
dnapath2-package        A short title line describing what the package
                        does
entrez_to_symbol        Obtain gene symbols for entrezgene IDs
filter_pathways         Remove pathways with non-significant DC scores.
get_genes               Get the gene names from a differential network
                        analysis
get_min_alpha           Get the minimum alpha level for the permutation
                        test
get_networks            Get the two association networks
get_reactome_pathways   Obtain Reactome pathways
head.dnapath_list       Return the first part of the dnapath results.
length.dnapath_list     The number of pathways in a 'dnapath_list'
                        object.
meso                    Gene expression dataset for two groups
names.dnapath           The pathway names in a 'dnapath' object.
names.dnapath_list      The pathway names in a 'dnapath_list' object.
p53_pathways            Reactome pathway list for Homo sapiens
plot.dnapath            Plot function for 'dnapath' object.
plot_pair               Plot the expression values of two genes
print.dnapath           Print function for 'dnapath' object.
print.dnapath_list      Print function for 'dnapath_list' object.
rename_genes            Rename genes in the differential network
                        analysis
rev.dnapath_list        Reverse the order of pathways in a
                        'dnapath_list' object.
run_aracne              Wrapper for ARACNE method
run_bc3net              Wrapper for BC3Net method
run_c3net               Wrapper for C3Net method
run_clr                 Wrapper for CLR method
run_corr                Wrapper for correlation co-expression
run_dwlasso             Wrapper for degree-weighted lasso method
run_genie3              Wrapper for GENIE3 method
run_glasso              Wrapper for glasso method
run_mrnet               Wrapper for MRNET method
run_pcor                Wrapper for partial correlations from corpcor
run_pcor_fdr            Wrapper for partial correlations with Empirical
                        Bayes FDR correction
run_silencer            Wrapper for silencer method
sort.dnapath_list       Sort function for 'dnapath_list' object.
subset.dnapath_list     Subset function for 'dnapath_list' object.
summarize_edges         Summarize differential connections for a
                        pathway
summarize_genes         Summarize the differential connectivity of
                        genes over all pathways.
summarize_pathways      Summarize the differential connectivity of
                        pathways.
summary.dnapath         Summary function for 'dnapath' object.
summary.dnapath_list    Summary function for 'dnapath_list' object.
symbol_to_entrez        Obtain entrezgene IDs for gene symbols
tail.dnapath_list       Return the last part of the dnapath results.
