Diffusion scores on biological networks

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Documentation for package ‘diffuStats’ version 1.24.0

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

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?