# Diffusion scores on biological networks

## Documentation for package ‘diffuStats’ version 1.14.0

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

## Help Pages

.available_methods | Sanity checks for input
.check_graph | Sanity checks for input
.check_K | Sanity checks for input
.check_method | Sanity checks for input
.check_metric | Sanity checks for input
.check_scores | Sanity checks for input
.connect_undirected_graph | Function to connect a non connected graph
.default_graph_param | Generate data.frame with default vertex attributes
.default_prop | Generate data.frame with default vertex attributes
commuteTimeKernel | Compute graph kernels
convertSparse | S4 sparse matrix to arma::sp_mat
diffuse | Diffuse scores on a network
diffuse_grid | Diffuse scores on a network
diffuse_mc | Compute the heatrank using permutations
diffuse_raw | Diffuse scores on a network
diffusionKernel | Compute graph kernels
diffuStats | diffuStats: an R package to compute and benchmark diffusion scores
generate_graph | Generate a random graph
generate_input | Generate a random input for graph diffusion
get_covar | Compute exact statistical moments
get_mu | Compute exact statistical moments
get_mu_reference | Compute exact statistical moments
get_var_reference | Compute exact statistical moments
graph_toy | Toy graph to play with diffusion
inverseCosineKernel | Compute graph kernels
is_kernel | Check if a matrix is a valid kernel
kernels | Compute graph kernels
largest_cc | Largest connected component
metric_auc | Compute the area under the curves (ROC, PRC)
metric_fun | Compute the area under the curves (ROC, PRC)
moments | Compute exact statistical moments
named.list | Create a named list
ParallelHeatrank | Compute heatrank in parallel
perf | Compare diffusions to a target score on a grid of parameters
perf_eval | Compute performance of diffusion scores on a single case
perf_wilcox | Compute column-wise statistics in a performance matrix
pStepKernel | Compute graph kernels
regularisedLaplacianKernel | Compute graph kernels
scores2colours | Translate values into colours
scores2shapes | Translate values into shapes
serialHeatrank | Compute heatrank for a single case
sparsify2 | Sparsify arma::mat into arma::sp_mat
to_list | Convert input to list format
to_x_from_list | Convert list format to desired format
which_format | In which format is the input?