Spatial Analysis of Network Associations


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Documentation for package ‘SANTA’ version 1.4.0

Help Pages

BinGraph Compute a distance bin matrix from a distance matrix.
CheckAttributes Check that a graph is associated with the correct vertex and edge attributes and can be passed to the 'Knet' and 'Knode' function.
CreateGraph Generate a simple undirected graph, with or without vertex weights and edge distances.
CreateGrid Generate a grid-like graph.
DistGraph Compute the vertex pair distance matrix of a graph.
GraphDiffusion Compute the distances between vertex pairs using a diffusion kernel-based method.
GraphMFPT Compute the distances between vertex pairs using a mean first-passage time-based method.
Kfct Compute statistics central to 'Knet' and 'Knode' functions.
Knet Measure the strength of association between a phenotype and a network by computing the strength of hit clustering on the network.
Knode Rank vertices by their strength of association with high-weight vertices.
MarkovCentrality Compute the Markov centrality score for each vertex in a graph.
plot.Knet Plot the results of the Knet function.
SpreadHits Spread hits across a graph.
treated.dataframe Edges from the genetic interaction network created by Bandyopadhyay et al. (2010) using yeast treated with the DNA-damaging agent methyl methanesulfonate (MMS)
untreated.dataframe Edges from the genetic interaction network created by Bandyopadhyay et al. (2010) using yeast under normal laboratory conditions.