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dnapath (version 0.7.4)

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

0.7.4

License

GPL-2 | GPL-3

Maintainer

Tyler Grimes

Last Published

May 9th, 2022

Functions in dnapath (0.7.4)

d_edgesC

C++ implementation of d_edges
dnapath

Differential Network Analysis Using Gene Pathways
d_genesC

C++ implementation of d_genes
c.dnapath_list

Combine two 'dnapath_list' objects.
entrez_to_symbol

Obtain gene symbols for entrezgene IDs
meso

Gene expression dataset for two groups
get_min_alpha

Get the minimum alpha level for the permutation test
c.dnapath

Combine two 'dnapath' objects.
names.dnapath

The pathway names in a 'dnapath' object.
get_networks

Get the two association networks
plot.dnapath

Plot function for 'dnapath' object.
filter_pathways

Remove pathways with non-significant DC scores.
init_mart

Initialize biomaRt for a given species
run_genie3

Wrapper for GENIE3 method
length.dnapath_list

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

Wrapper for glasso method
format_species_name

Format sepcies name input.
get_genes

Get the gene names from a differential network analysis
names.dnapath_list

The pathway names in a 'dnapath_list' object.
run_corr

Wrapper for correlation co-expression
run_c3net

Wrapper for C3Net method
plot_pair

Plot the expression values of two genes
run_clr

Wrapper for CLR method
get_mean_expr_mat

Get mean expression of pathway genes in both groups
get_biomart_mapping

Internal function for obtaining biomaRt mapping
run_pcor_fdr

Wrapper for partial correlations with Empirical Bayes FDR correction
run_mrnet

Wrapper for MRNET method
get_reactome_pathways

Obtain Reactome pathways
p53_pathways

Reactome pathway list for Homo sapiens
sort.dnapath_list

Sort 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_pcor

Wrapper for partial correlations from corpcor
summarize_pathways

Summarize the differential connectivity of pathways.
head.dnapath_list

Return the first part of the dnapath results.
summarize_genes_for_pathway

Summarize differential connectivity of genes in a pathway
print.dnapath

Print function for 'dnapath' object.
run_dwlasso

Wrapper for degree-weighted lasso method
[[.dnapath_list

Extract results of a single pathway from a 'dnapath_list' object.
symbol_to_entrez

Obtain entrezgene IDs for gene symbols
tail.dnapath_list

Return the last part of the dnapath results.
run_silencer

Wrapper for silencer method
summarize_edges

Summarize differential connections for a pathway
[.dnapath

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

Summarize the differential connectivity of genes over all pathways.
[<-.dnapath

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

Subset function for 'dnapath_list' object.
[<-.dnapath_list

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

Print function for 'dnapath_list' object.
run_aracne

Wrapper for ARACNE method
summary.dnapath_list

Summary function for 'dnapath_list' object.
summary.dnapath

Summary function for 'dnapath' object.
run_bc3net

Wrapper for BC3Net method
[[.dnapath

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

Extract parts of a 'dnapath_list' object.
biomart_hsapiens

Default mapping for entrezgene IDs and HGNC gene symbols
combine_overlapping_pathways

Modify a pathway list to combine overlapping pathways.
d_pathwayC

C++ implementation of d_pathway
dnapath2-package

A short title line describing what the package does
dna_pathway

Differential network analysis on a single pathway