# Pathway Fingerprint Framework in R

## Documentation for package ‘PFP’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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