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| calc_PFP_score | Get the pathway fingerprint of a gene_list |
| data_std | A matrix of counts A dataset of gene expression profile, a large matrix with 21 rows and 2603 columns. |
| genes_score | The score of genes in _PFP_ class |
| genes_score-method | The score of genes in _PFP_ class |
| genes_score-methods | The score of genes in _PFP_ class |
| gene_list_hsa | A gene list of human gene_list_hsa is a array of 40 genetic ENTREZID. |
| get_asso_net | merge the edges_coexp and edges_kegg |
| get_bg_related_kegg | get_bg_related_kegg |
| get_exp_cor_edges | get co-expression genes |
| get_pathway_info | get pathway info of a species in KEGG |
| get_PFPRefnet | get a PFPRefnet for a species |
| group | group information of _PFPRefnet_ |
| group-method | group information of _PFPRefnet_ |
| group-methods | group information of _PFPRefnet_ |
| kegg_download | download kegg KGML files |
| network | Basic pathway networks of _PFPRefnet_ class |
| network-method | Basic pathway networks of _PFPRefnet_ class |
| network-methods | Basic pathway networks of _PFPRefnet_ class |
| net_info | Basic pathway networks information of _PFPRefnet_ class |
| net_info-method | Basic pathway networks information of _PFPRefnet_ class |
| net_info-methods | Basic pathway networks information of _PFPRefnet_ class |
| net_names | Names of basic networks |
| net_names-method | Names of basic networks |
| net_names-methods | Names of basic networks |
| pathways_score | Basic pathway networks scores of _PFP_ class |
| pathways_score-method | Basic pathway networks scores of _PFP_ class |
| pathways_score-methods | Basic pathway networks scores of _PFP_ class |
| pathway_info | pathway_info pathway_info is dataframe of the information of pathway, 539rows, 4columns. |
| pathway_info_hsa | pathway_info pathway_info is dataframe of the information of pathway, 539rows, 4columns. |
| PFP | The NFP package |
| PFP-class | 'PFP-class' |
| PFPRefnet-class | 'PFPRefnet-class' |
| PFPRefnet_hsa | Pathway fingerprint data of human |
| PFPRefnet_mmu | Pathway fingerprint data of mouse |
| PFP_score | The score of _PFP_ |
| PFP_score-method | The score of _PFP_ |
| PFP_score-methods | The score of _PFP_ |
| PFP_test1 | PFP_test1 |
| PFP_test2 | PFP_test2 |
| plot_PFP | Plot PFP results |
| plot_PFP-method | Plot PFP results |
| plot_PFP-methods | Plot PFP results |
| plot_PFPlist | Plot multiple PFPs. |
| rank_PFP | rank PFPscore |
| rank_PFP-method | rank PFPscore |
| rank_PFP-methods | rank PFPscore |
| refnet_info | Basic network information of _PFP_ class |
| refnet_info-method | Basic network information of _PFP_ class |
| refnet_info-methods | Basic network information of _PFP_ class |
| refnet_names | Names of basic networks |
| refnet_names-method | Names of basic networks |
| refnet_names-methods | Names of basic networks |
| result_PFP | result of the PFP object. |
| result_PFP-method | result of the PFP object. |
| result_PFP-methods | result of the PFP object. |
| show_net | Show an Object |
| show_net-method | Show an Object |
| show_net-methods | Show an Object |
| show_PFP | The show_PFP generic function |
| show_PFP-method | The show_PFP generic function |
| show_PFP-methods | The show_PFP generic function |
| stats_test | The P value of _PFP_ |
| stats_test-method | The P value of _PFP_ |
| stats_test-methods | The P value of _PFP_ |
| subnet | Subset the basic networks |
| subnet-method | Subset the basic networks |
| subnet-methods | Subset the basic networks |
| sub_PFP | subset of PFP object |
| sub_PFP-method | subset of PFP object |
| sub_PFP-methods | subset of PFP object |
| trans_edges_id | trans_edges_id |
| trans_graph2PFPRefnet | translate graph_list to PFPRefnet class |
| trans_xml2graph | translate kgml files to graphNEl |