# Differential Network Analysis using Gene Pathways

## Documentation for package ‘dnapath’ version 0.6.11

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

## Help Pages

dnapath2-package | A short title line describing what the package does
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.
dnapath | Differential Network Analysis Using Gene Pathways
dnapath2 | A short title line describing what the package does
d_edgesC | C++ implementation of d_edges
d_genesC | C++ implementation of d_genes
d_pathwayC | C++ implementation of d_pathway
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.
[.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.