Pathway Fingerprint Framework in R

---

Documentation for package ‘PFP’ version 1.6.0

• 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