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dnapath (version 0.7.6)

Differential Network Analysis using Gene Pathways

Description

Integrates pathway information into the differential network analysis of two gene expression datasets as described in Grimes, Potter, and Datta (2019) . 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.

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Version

Install

install.packages('dnapath')

Monthly Downloads

140

Version

0.7.6

License

GPL-2 | GPL-3

Maintainer

Tyler Grimes

Last Published

February 21st, 2025

Functions in dnapath (0.7.6)

get_mean_expr_mat

Get mean expression of pathway genes in both groups
head.dnapath_list

Return the first part of the dnapath results.
get_min_alpha

Get the minimum alpha level for the permutation test
get_reactome_pathways

Obtain Reactome pathways
init_mart

Initialize biomaRt for a given species
get_genes

Get the gene names from a differential network analysis
get_biomart_mapping

Internal function for obtaining biomaRt mapping
print.dnapath_list

Print function for 'dnapath_list' object.
rename_genes

Rename genes in the differential network analysis
names.dnapath

The pathway names in a 'dnapath' object.
names.dnapath_list

The pathway names in a 'dnapath_list' object.
run_pcor

Wrapper for partial correlations from corpcor
run_mrnet

Wrapper for MRNET method
run_genie3

Wrapper for GENIE3 method
run_glasso

Wrapper for glasso method
plot_pair

Plot the expression values of two genes
rev.dnapath_list

Reverse the order of pathways in a 'dnapath_list' object.
run_aracne

Wrapper for ARACNE method
print.dnapath

Print function for 'dnapath' object.
run_bc3net

Wrapper for BC3Net method
run_c3net

Wrapper for C3Net method
p53_pathways

Reactome pathway list for Homo sapiens
run_corr

Wrapper for correlation co-expression
sort.dnapath_list

Sort function for 'dnapath_list' object.
summarize_genes_for_pathway

Summarize differential connectivity of genes in a pathway
length.dnapath_list

The number of pathways in a 'dnapath_list' object.
plot.dnapath

Plot function for 'dnapath' object.
meso

Gene expression dataset for two groups
run_clr

Wrapper for CLR method
run_pcor_fdr

Wrapper for partial correlations with Empirical Bayes FDR correction
[.dnapath_list

Extract parts of a 'dnapath_list' object.
[.dnapath

Extract results of a single pathway from a 'dnapath' object.
[[.dnapath

Extract results of a single pathway from a 'dnapath' object.
summarize_pathways

Summarize the differential connectivity of pathways.
summarize_edges

Summarize differential connections for a pathway
summarize_genes

Summarize the differential connectivity of genes over all pathways.
summary.dnapath

Summary function for 'dnapath' object.
[[.dnapath_list

Extract results of a single pathway from a 'dnapath_list' object.
[<-.dnapath_list

Replace parts of a 'dnapath_list' object.
[<-.dnapath

Replace parts of a 'dnapath' object.
tail.dnapath_list

Return the last part of the dnapath results.
subset.dnapath_list

Subset function for 'dnapath_list' object.
symbol_to_entrez

Obtain entrezgene IDs for gene symbols
summary.dnapath_list

Summary function for 'dnapath_list' object.
run_silencer

Wrapper for silencer method
c.dnapath

Combine two 'dnapath' objects.
c.dnapath_list

Combine two 'dnapath_list' objects.
d_genesC

C++ implementation of d_genes
dnapath

Differential Network Analysis Using Gene Pathways
biomart_hsapiens

Default mapping for entrezgene IDs and HGNC gene symbols
d_pathwayC

C++ implementation of d_pathway
entrez_to_symbol

Obtain gene symbols for entrezgene IDs
d_edgesC

C++ implementation of d_edges
dna_pathway

Differential network analysis on a single pathway
combine_overlapping_pathways

Modify a pathway list to combine overlapping pathways.
filter_pathways

Remove pathways with non-significant DC scores.
get_networks

Get the two association networks
format_species_name

Format sepcies name input.