Diffusion scores on biological networks

[Up] [Top]

Documentation for package ‘diffuStats’ version 0.102.0

Help Pages

diffuStats-package diffuStats: an R package to compute and benchmark diffusion scores
.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
graph_toy Toy graph to play with diffusion
inverseCosineKernel Compute graph kernels
is_kernel Check if a matrix is a valid kernel
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)
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?