NFP: Network Fingerprint Framework in R
Version 0.99.2

An implementation of the network fingerprint framework that introduced in paper "Network fingerprint: a knowledge-based characterization of biomedical networks" (Cui, 2015) . This method worked by making systematic comparisons to a set of well-studied "basic networks", measuring both the functional and topological similarity. A biological could be characterized as a spectrum-like vector consisting of similarities to basic networks. It shows great potential in biological network study.

AuthorYang Cao [aut, cre], Fei Li [aut]
Date of publication2016-11-21 12:01:34
MaintainerYang Cao <yiluheihei@gmail.com>
LicenseGPL (>= 2)
Version0.99.2
URL https://github.com/yiluheihei/NFP
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("NFP")

Getting started

README.md

Popular man pages

calc_sim_score: Calculating the similarity scores
net-methods: Basic networks of _NFPRefnet_ class
NFP-class: 'NFP-class'
plot_NFP-methods: Plot NFP results
show-methods: The show generic function
show_NFPRefnet-methods: Show an Object
subnet-methods: Subset the basic networks
See all...

All man pages Function index File listing

Man pages

calc_sim_score: Calculating the similarity scores
cluster_info-methods: Extract the cluster information of _NFP_.
group-methods: Group information of _NFPRefnet_
install_data_package: Install NFP data package NFPdata
kegg_refnet: Human KEGG signal pathway maps
load_KEGG_refnet: Load the the reference molecular networks
net-methods: Basic networks of _NFPRefnet_ class
NFP: The NFP package
NFP-class: 'NFP-class'
NFPRefnet-class: 'NFPRefnet-class'
perm_score-methods: Extract the randomized similarity score
plot_NFPlist: Plot multiple NFPs.
plot_NFP-methods: Plot NFP results
refnet_name-methods: Names of basic networks
show-methods: The show generic function
show_NFPRefnet-methods: Show an Object
subnet-methods: Subset the basic networks
sub_NFP-methods: subset of NFP object

Functions

NFP Man page
NFP-class Man page
NFP-package Man page
NFPRefnet-class Man page
calc_sim_score Man page Source code
check.NFP Source code
check.NFPRefnet Source code
cluster_info Man page
cluster_info,NFP-method Man page
cluster_info-methods Man page
getPathwayList Source code
group Man page
group,NFPRefnet-method Man page
group-methods Man page
install_data_package Man page Source code
kegg_refnet Man page
load_KEGG_refnet Man page Source code
net Man page
net,NFPRefnet-method Man page
net-methods Man page
onLoad Source code
perm_score Man page
perm_score,NFP-method Man page
perm_score-methods Man page
plot_NFP Man page
plot_NFP,NFP-method Man page
plot_NFP-methods Man page
plot_NFPlist Man page Source code
plotnfp Source code
refnet_name Man page
refnet_name,NFPRefnet-method Man page
refnet_name-methods Man page
show Man page
show,NFP-method Man page
show,NFPRefnet-method Man page
show-methods Man page
show_NFPRefnet Man page
show_NFPRefnet-methods Man page
sub_NFP Man page
sub_NFP,NFP-method Man page
sub_NFP-methods Man page
subnet Man page
subnet,NFPRefnet-method Man page
subnet-methods Man page

Files

inst
inst/extdata
inst/extdata/signalPathway.txt
inst/extdata/humanPathway.txt
inst/doc
inst/doc/NFP.pdf
inst/doc/NFP.Rnw
inst/doc/NFP.R
tests
tests/testthat.R
tests/testthat
tests/testthat/test-NFP.R
tests/testthat/test-NFPRefnet.R
NAMESPACE
data
data/datalist
data/kegg_refnet.rda
R
R/NFP-class.R
R/Untitled.R
R/load_KEGG_refnet.R
R/kegg_refnet.R
R/plot_NFPlist.R
R/NFP.R
R/calc_sim_score.R
R/install_data_package.R
R/zzz.R
R/NFPRefnet-class.R
vignettes
vignettes/NFP.Rnw
vignettes/nfp_plot.png
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/NFPRefnet-class.Rd
man/cluster_info-methods.Rd
man/calc_sim_score.Rd
man/NFP-class.Rd
man/net-methods.Rd
man/show_NFPRefnet-methods.Rd
man/plot_NFPlist.Rd
man/load_KEGG_refnet.Rd
man/kegg_refnet.Rd
man/subnet-methods.Rd
man/perm_score-methods.Rd
man/group-methods.Rd
man/sub_NFP-methods.Rd
man/NFP.Rd
man/install_data_package.Rd
man/plot_NFP-methods.Rd
man/refnet_name-methods.Rd
man/show-methods.Rd
NFP documentation built on May 20, 2017, 2:08 a.m.

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