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dnapath (version 0.6.4)

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

87

Version

0.6.4

License

GPL-2 | GPL-3

Maintainer

Tyler Grimes

Last Published

July 9th, 2020

Functions in dnapath (0.6.4)

dnapath2-package

A short title line describing what the package does
rev.dnapath_list

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

Wrapper for silencer method
[.dnapath

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

Wrapper for partial correlations from corpcor
sort.dnapath_list

Sort function for 'dnapath_list' object.
d_edgesC

C++ implementation of d_edges
run_aracne

Wrapper for ARACNE method
combine_overlapping_pathways

Modify a pathway list to combine overlapping pathways.
entrez_to_symbol

Obtain gene symbols for entrezgene IDs
print.dnapath_list

Print function for 'dnapath_list' object.
get_mean_expr_mat

Get mean expression of pathway genes in both groups
rename_genes

Rename genes in the differential network analysis
get_min_alpha

Get the minimum alpha level for the permutation test
run_dwlasso

Wrapper for degree-weighted lasso method
head.dnapath_list

Return the first part of the dnapath results.
run_genie3

Wrapper for GENIE3 method
init_mart

Initialize biomaRt for mmusculus
[<-.dnapath_list

Replace parts of a 'dnapath_list' object.
names.dnapath_list

The pathway names in a 'dnapath_list' object.
run_clr

Wrapper for CLR method
names.dnapath

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

Subset function for 'dnapath_list' object.
run_corr

Wrapper for correlation co-expression
dnapath

Differential Network Analysis Using Gene Pathways
get_networks

Get the two association networks
get_reactome_pathways

Obtain Reactome pathways
[[.dnapath_list

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

Replace parts of a 'dnapath' object.
symbol_to_entrez

Obtain entrezgene IDs for gene symbols
plot_pair

Plot the expression values of two genes
tail.dnapath_list

Return the last part of the dnapath results.
d_genesC

C++ implementation of d_genes
d_pathwayC

C++ implementation of d_pathway
length.dnapath_list

The number of pathways in a 'dnapath_list' object.
p53_pathways

Reactome pathway list for Homo sapiens
plot.dnapath

Plot function for 'dnapath' object.
run_glasso

Wrapper for glasso method
print.dnapath

Print function for 'dnapath' object.
run_bc3net

Wrapper for BC3Net method
meso

Gene expression dataset for two groups
run_c3net

Wrapper for C3Net method
summarize_edges

Summarize differential connections for a pathway
run_mrnet

Wrapper for MRNET method
summarize_genes

Summarize the differential connectivity of genes over all pathways.
summarize_pathways

Summarize the differential connectivity of pathways.
summarize_genes_for_pathway

Summarize differential connectivity of genes in a pathway
summary.dnapath

Summary function for 'dnapath' object.
summary.dnapath_list

Summary function for 'dnapath_list' object.
[.dnapath_list

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

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

Combine two 'dnapath' objects.
c.dnapath_list

Combine two 'dnapath_list' objects.
filter_pathways

Remove pathways with non-significant DC scores.
get_genes

Get the gene names from a differential network analysis
dna_pathway

Differential network analysis on a single pathway