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. |