Man pages for tgrimes/dnapath2
Differential Network Analysis Using Gene Pathways
| 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 |
| dnapath2-package | A short title line describing what the package does |
| d_pathwayC | C++ implementation of d_pathway |
| fdr | Determine which associations are significant |
| filter_pathways | Remove pathways with non-significant DC scores. |
| get_min_alpha | Get the minimum alpha level for the permutation test |
| get_reactome_pathways | Obtain reactome pathways |
| head.dnapath_list | Return the first five pathways of a 'dnapath_list' object. |
| order.dnapath_list | Order function for 'dnapath_list' object. |
| plot.dnapath | Plot function for 'dnapath' object. |
| 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 results |
| rev.dnapathpath_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 C3Net method |
| run_glasso | Wrapper for glasso method |
| run_mrnet | Wrapper for MRNET method |
| run_pcor | Wrapper for partial correlations from corpcor |
| run_silencer | Wrapper for silencer method |
| sort.dnapath_list | Sort function for 'dnapath_list' object. |
| sub-.dnapath_list | Extract parts of a 'dnapath_list' object. |
| subset-.dnapath_list | Replace parts of a 'dnapath_list' object. |
| subset.dnapath_list | Subset function for 'dnapath_list' object. |
| summarize_dnw_for_pathway | Summarize differential connectivity scores for a pathway |
| summarize_edges_for_pathway | 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. |
| tail.dnapath_list | Return the last five pathways of a 'dnapath_list' object. |
| vector_to_matrix | Turn a vector into a matrix |
