Construct a Shared Nearest Neighbor (SNN) Graph for a given dataset.
BuildSNN(object, genes.use = NULL, pc.use = NULL, k.param = 10,
k.scale = 10, plot.SNN = FALSE, prune.SNN = 1/15, do.sparse = FALSE,
print.output = TRUE)
Seurat object
Gene expression data
Which PCs to use for construction of the SNN graph
Defines k for the k-nearest neighbor algorithm
granularity option for k.param
Plot the SNN graph
Stringency of pruning for the SNN graph (0 - no pruning, 1 - prune everything)
Whether to compute and return the SNN graph as a sparse matrix or not
Whether or not to print output to the console
Returns the object with object@snn.k and either object@snn.dense or object@snn.sparse filled depending on the option set