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-methods       The score of _PFP_
PFP_test1               PFP_test1
PFP_test2               PFP_test2
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.
gene_list_hsa           A gene list of human gene_list_hsa is a array
                        of 40 genetic ENTREZID.
genes_score-methods     The score of genes in _PFP_ class
get_PFPRefnet           get a PFPRefnet for a species
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
group-methods           group information of _PFPRefnet_
kegg_download           download kegg KGML files
net_info-methods        Basic pathway networks information of
                        _PFPRefnet_ class
net_names-methods       Names of basic networks
network-methods         Basic pathway networks of _PFPRefnet_ 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.
pathways_score-methods
                        Basic pathway networks scores of _PFP_ class
plot_PFP-methods        Plot PFP results
plot_PFPlist            Plot multiple PFPs.
rank_PFP-methods        rank PFPscore
refnet_info-methods     Basic network information of _PFP_ class
refnet_names-methods    Names of basic networks
result_PFP-methods      result of the PFP object.
show_PFP                The show_PFP generic function
show_net                Show an Object
stats_test-methods      The P value of _PFP_
sub_PFP-methods         subset of PFP object
subnet-methods          Subset the basic networks
trans_edges_id          trans_edges_id
trans_graph2PFPRefnet   translate graph_list to PFPRefnet class
trans_xml2graph         translate kgml files to graphNEl
