Man pages for dnapath
Differential Network Analysis using Gene Pathways
| 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. |
| combine_overlapping_pathways | Modify a pathway list to combine overlapping pathways. |
| d_edgesC | C++ implementation of d_edges |
| d_genesC | C++ implementation of d_genes |
| dnapath | Differential Network Analysis Using Gene Pathways |
| dnapath2-package | A short title line describing what the package does |
| dna_pathway | Differential network analysis on a single pathway |
| 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. |
| format_species_name | Format sepcies name input. |
| get_biomart_mapping | Internal function for obtaining biomaRt mapping |
| get_genes | Get the gene names from a differential network analysis |
| get_mean_expr_mat | Get mean expression of pathway genes in both groups |
| 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. |
| init_mart | Initialize biomaRt for a given species |
| 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... |
| run_silencer | Wrapper for silencer method |
| sort.dnapath_list | Sort function for 'dnapath_list' object. |
| sub-.dnapath | Extract results of a single pathway from a 'dnapath' object. |
| sub-.dnapath_list | Extract parts of a 'dnapath_list' object. |
| subset-.dnapath | Replace parts of a 'dnapath' object. |
| subset-.dnapath_list | Replace parts of a 'dnapath_list' object. |
| subset.dnapath_list | Subset function for 'dnapath_list' object. |
| sub-sub-.dnapath | Extract results of a single pathway from a 'dnapath' object. |
| sub-sub-.dnapath_list | Extract results of a single pathway from a 'dnapath_list'... |
| summarize_edges | Summarize differential connections for a pathway |
| summarize_genes | Summarize the differential connectivity of genes over all... |
| summarize_genes_for_pathway | Summarize differential connectivity of genes in a pathway |
| 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. |
