Integration of Disease Similarity Methods

Documentation for package ‘dSimer’ version 1.4.0

Help Pages

dSimer-package	Integration of Disease Similarity Methods
BOG	calculate disease similarity by BOG
CosineDFV	calculate disease similarity by using feature vectors
d2go_sample	d2go_sample
d2g_fundo_entrezid	d2g_fundo_entrezid
d2g_fundo_symbol	d2g_fundo_symbol
d2g_separation	d2g_separation
d2s_hsdn	d2s_hsdn
d2s_hsdn_sample	d2s_hsdn_sample
dSimer	Integration of Disease Similarity Methods
FunSim	calculate disease similarity by FunSim
get_GOterm2GeneAssos	get GO-gene associations
go2g_sample	go2g_sample
graphlet_sig_hprd	graphlet_sig_hprd
HumanNet_sample	HumanNet_sample
HypergeometricTest	Hypergeometric test and multiple testing
ICod	calculate disease similarity by ICod
InformationContent	calculating information content
interactome	interactome
jaccardindex	calculating Jaccard Index
LLSn2List	convert data.frame of HumanNet log-likelihood Score to list
Normalize	normalize data
orbit_dependency_count	orbit_dependency_count
plot_bipartite	plot disease-gene (or GO term etc.) associations as a bipartite graph
plot_heatmap	similarity matrix heatmap plotting
plot_net	plot a network based on a symmetric disease similarity matrix
plot_topo	plot topological relationship of two gene sets
PPI_HPRD	PPI_HPRD
PSB	calculate disease similarity by PSB
Separation	calculating network-based separation of disease pairs
Separation2Similarity	a method which convert separation to similarity
setWeight	set weight factor
Sun_annotation	Sun's annotation measure of disease similarity calculating
Sun_function	Sun's function measure of disease similarity calculating
Sun_topology	Sun's topology measure of disease similarity calculating
weight	weight
x2y_conv2_y2x	convert x2ylist to y2xlist
x2y_df2list	convert x-y associations