Man pages for dnapath
Differential Network Analysis using Gene Pathways

biomart_hsapiensDefault mapping for entrezgene IDs and HGNC gene symbols
c.dnapathCombine two 'dnapath' objects.
c.dnapath_listCombine two 'dnapath_list' objects.
combine_overlapping_pathwaysModify a pathway list to combine overlapping pathways.
d_edgesCC++ implementation of d_edges
d_genesCC++ implementation of d_genes
dnapathDifferential Network Analysis Using Gene Pathways
dnapath2-packageA short title line describing what the package does
dna_pathwayDifferential network analysis on a single pathway
d_pathwayCC++ implementation of d_pathway
entrez_to_symbolObtain gene symbols for entrezgene IDs
filter_pathwaysRemove pathways with non-significant DC scores.
format_species_nameFormat sepcies name input.
get_biomart_mappingInternal function for obtaining biomaRt mapping
get_genesGet the gene names from a differential network analysis
get_mean_expr_matGet mean expression of pathway genes in both groups
get_min_alphaGet the minimum alpha level for the permutation test
get_networksGet the two association networks
get_reactome_pathwaysObtain Reactome pathways
head.dnapath_listReturn the first part of the dnapath results.
init_martInitialize biomaRt for a given species
length.dnapath_listThe number of pathways in a 'dnapath_list' object.
mesoGene expression dataset for two groups
names.dnapathThe pathway names in a 'dnapath' object.
names.dnapath_listThe pathway names in a 'dnapath_list' object.
p53_pathwaysReactome pathway list for Homo sapiens
plot.dnapathPlot function for 'dnapath' object.
plot_pairPlot the expression values of two genes
print.dnapathPrint function for 'dnapath' object.
print.dnapath_listPrint function for 'dnapath_list' object.
rename_genesRename genes in the differential network analysis
rev.dnapath_listReverse the order of pathways in a 'dnapath_list' object.
run_aracneWrapper for ARACNE method
run_bc3netWrapper for BC3Net method
run_c3netWrapper for C3Net method
run_clrWrapper for CLR method
run_corrWrapper for correlation co-expression
run_dwlassoWrapper for degree-weighted lasso method
run_genie3Wrapper for GENIE3 method
run_glassoWrapper for glasso method
run_mrnetWrapper for MRNET method
run_pcorWrapper for partial correlations from corpcor
run_pcor_fdrWrapper for partial correlations with Empirical Bayes FDR...
run_silencerWrapper for silencer method
sort.dnapath_listSort function for 'dnapath_list' object.
sub-.dnapathExtract results of a single pathway from a 'dnapath' object.
sub-.dnapath_listExtract parts of a 'dnapath_list' object.
subset-.dnapathReplace parts of a 'dnapath' object.
subset-.dnapath_listReplace parts of a 'dnapath_list' object.
subset.dnapath_listSubset function for 'dnapath_list' object.
sub-sub-.dnapathExtract results of a single pathway from a 'dnapath' object.
sub-sub-.dnapath_listExtract results of a single pathway from a 'dnapath_list'...
summarize_edgesSummarize differential connections for a pathway
summarize_genesSummarize the differential connectivity of genes over all...
summarize_genes_for_pathwaySummarize differential connectivity of genes in a pathway
summarize_pathwaysSummarize the differential connectivity of pathways.
summary.dnapathSummary function for 'dnapath' object.
summary.dnapath_listSummary function for 'dnapath_list' object.
symbol_to_entrezObtain entrezgene IDs for gene symbols
tail.dnapath_listReturn the last part of the dnapath results.
dnapath documentation built on May 9, 2022, 9:05 a.m.