Differential Network Analysis using Gene Pathways

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Documentation for package ‘dnapath’ version 0.7.4

• 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.