# Integration of Disease Similarity Methods

## Documentation for package ‘dSimer’ version 1.0.0

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

## 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