BuildSNN: SNN Graph Construction

In nukappa/seurat_v2: Seurat : R toolkit for single cell genomics

Description

Construct a Shared Nearest Neighbor (SNN) Graph for a given dataset.

Usage

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)

Arguments

object	Seurat object
genes.use	Gene expression data
pc.use	Which PCs to use for construction of the SNN graph
k.param	Defines k for the k-nearest neighbor algorithm
k.scale	granularity option for k.param
plot.SNN	Plot the SNN graph
prune.SNN	Stringency of pruning for the SNN graph (0 - no pruning, 1 - prune everything)
do.sparse	Whether to compute and return the SNN graph as a sparse matrix or not
print.output	Whether or not to print output to the console

Value

Returns the object with object@snn.k and either [e-mail] or [e-mail] filled depending on the option set

nukappa/seurat_v2 documentation built on May 24, 2019, 9:57 a.m.